minimal Common Oncology Data Elements (mCODE) Implementation Guide
3.0.0 - STU3 Release United States of America flag

This page is part of the HL7 FHIR Implementation Guide: minimal Common Oncology Data Elements (mCODE) Release 1 - US Realm | STU1 (v3.0.0: STU 3) based on FHIR R4. This is the current published version. For a full list of available versions, see the Directory of published versions

Resource Profile: Genomic Variant Profile

Official URL: http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-genomic-variant Version: 3.0.0
Draft as of 2023-10-26 Maturity Level: 1 Computable Name: GenomicVariant

Details about a set of changes in the tested sample compared to a reference sequence. The term variant can be used to describe an alteration that may be benign, pathogenic, or of unknown significance. The term variant is increasingly being used in place of the term mutation. Variants can be computed relative to reference sequence assembly from which it was identified.

Usage

GenomicVariant SHOULD be sent as part of a GenomicsReport and MAY be sent as a standalone observation.

Conformance

Observation resources associated with an in-scope patient with Observation.code LOINC 69548-6 SHALL conform to this profile. Beyond this requirement, a producer of resources SHOULD ensure that any resource instance associated with an in-scope patient that would reasonably be expected to conform to this profile SHOULD be published in this form.

Usage:

Formal Views of Profile Content

Description of Profiles, Differentials, Snapshots and how the different presentations work.

This structure is derived from Variant

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation 0..*VariantVariant
... status S1..1coderegistered | preliminary | final | amended +
... category S1..*CodeableConceptClassification of type of observation
... category:labCategory 1..1CodeableConceptClassification of type of observation
Required Pattern: At least the following
.... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
..... system1..1uriIdentity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
..... code1..1codeSymbol in syntax defined by the system
Fixed Value: laboratory
.... coding 1..1CodingCode defined by a terminology system
... subject S0..1Reference(Cancer Patient Profile)Who and/or what the observation is about
... Slices for effective[x] S0..1dateTime, Period, Timing, instantClinically relevant time/time-period for observation
Slice: Unordered, Open by type:$this
.... effective[x]:effectiveDateTime S0..1dateTimeClinically relevant time/time-period for observation
... value[x] S0..1CodeableConceptActual result
... dataAbsentReason S0..1CodeableConceptWhy the result is missing
... method S0..1CodeableConceptSequencing | SNP array | PCR | Computational analysis | ...
... specimen S0..1Reference(Human Specimen Profile)Specimen used for this observation
... referenceRange 0..*BackboneElementNot used in this profile
... hasMember 0..*Reference(Observation | QuestionnaireResponse | MolecularSequence)Not used in this profile
... component S0..*BackboneElementComponent results
... component:gene-studied S0..*BackboneElementGene Studied
.... code S1..1CodeableConcept48018-6
.... value[x] S1..1CodeableConceptThe HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used.
... component:cytogenetic-location S0..*BackboneElementCytogenetic (Chromosome) Location
.... code S1..1CodeableConcept48001-2
.... value[x] S1..1CodeableConceptExample: 1q21.1
... component:genomic-hgvs S0..1BackboneElementGenomic (gDNA) Change - gHGVS
.... code S1..1CodeableConcept81290-9
.... value[x] S1..1CodeableConceptA valid HGVS-formatted 'g.' string, e.g. NC_000016.9:g.2124200_2138612dup
... component:cytogenomic-nomenclature S0..1BackboneElementCytogenomic Nomenclature (ISCN)
.... code S1..1CodeableConcept81291-7
.... value[x] S1..1CodeableConceptActual component result
... component:coding-change-type S0..1BackboneElementCoding DNA Change Type
.... code S1..1CodeableConcept48019-4
.... value[x] S1..1CodeableConceptdeletion | insertion | delins | SNV | copy_number_gain | copy_number_loss | ... (many)
... component:genomic-source-class S0..1BackboneElementGenomic Source Class
.... code S1..1CodeableConcept48002-0
.... value[x] S1..1CodeableConceptGermline | Somatic | Fetal | Likely germline | Likely somatic | Likely fetal | Unknown genomic origin | De novo
... component:sample-allelic-frequency S0..1BackboneElementSample Allelic Frequency
.... code S1..1CodeableConcept81258-6
.... value[x] S0..1QuantityRelative frequency in the sample
... component:allelic-state S0..1BackboneElementAllelic State
.... code S1..1CodeableConcept53034-5
.... value[x] S1..1CodeableConceptHeteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous
... component:variation-code S0..*BackboneElementVariation Code
.... code S1..1CodeableConcept81252-9
.... value[x] S1..1CodeableConceptClinVar ID or similar
... component:protein-hgvs S0..1BackboneElementProtein (Amino Acid) Change - pHGVS
.... code S1..1CodeableConcept48005-3
.... value[x] S1..1CodeableConceptA valid HGVS-formatted 'p.' string, e.g. NP_000050.2:p.(Asn1836Lys)
... component:amino-acid-change-type S0..1BackboneElementAmino Acid Change Type
.... code S1..1CodeableConcept48006-1
.... value[x] S1..1CodeableConceptWild type | Deletion | Duplication | Frameshift | Initiating Methionine | Insertion | Insertion and Deletion | Missense | Nonsense | Silent
... component:molecular-consequence S0..1BackboneElementMolecular Consequence
.... code S1..1CodeableConceptmolecular-consequence
.... value[x] S1..1CodeableConceptstop_lost | stop_gained | inframe_insertion | frameshift_variant | ... (many)
... component:copy-number S0..1BackboneElementGenomic Structural Variant Copy Number
.... code S1..1CodeableConcept82155-3
.... value[x] S0..1QuantityActual component result

doco Documentation for this format
NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation C0..*VariantVariant
... implicitRules ?!Σ0..1uriA set of rules under which this content was created
... secondary-finding 0..1CodeableConceptSecondary findings are genetic test results that provide information about variants in a gene unrelated to the primary purpose for the testing, most often discovered when [Whole Exome Sequencing (WES)](https://en.wikipedia.org/wiki/Exome_sequencing) or [Whole Genome Sequencing (WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) is performed. This extension should be used to denote when a genetic finding is being shared as a secondary finding, and ideally refer to a corresponding guideline or policy statement. For more detail, please see: https://ghr.nlm.nih.gov/primer/testing/secondaryfindings
URL: http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding
Binding: GeneticObservationSecondaryFindings (extensible): Codes to denote a guideline or policy statement when a genetic test result is being shared as a secondary finding.


... body-structure 0..1Reference(BodyStructure)Target anatomic location or structure
URL: http://hl7.org/fhir/StructureDefinition/bodySite
... status ?!SΣ1..1coderegistered | preliminary | final | amended +
Binding: ObservationStatus (required): Codes providing the status of an observation.

... Slices for category S1..*CodeableConceptClassification of type of observation
Slice: Unordered, Open by value:coding
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.


.... category:labCategory 1..1CodeableConceptClassification of type of observation
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.



Required Pattern: At least the following
..... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
...... system1..1uriIdentity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
...... code1..1codeSymbol in syntax defined by the system
Fixed Value: laboratory
..... coding Σ1..1CodingCode defined by a terminology system

Required Pattern: At least the following
...... system1..1uriIdentity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
...... code1..1codeSymbol in syntax defined by the system
Fixed Value: laboratory
... code SΣ1..1CodeableConcept69548-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
.... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
..... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
..... code1..1codeSymbol in syntax defined by the system
Fixed Value: 69548-6
... subject SΣ0..1Reference(Cancer Patient Profile)Who and/or what the observation is about
... Slices for effective[x] SΣ0..1Clinically relevant time/time-period for observation
Slice: Unordered, Open by type:$this
.... effectiveDateTimedateTime
.... effectivePeriodPeriod
.... effectiveTimingTiming
.... effectiveInstantinstant
.... effective[x]:effectiveDateTime SΣ0..1dateTimeClinically relevant time/time-period for observation
... Slices for value[x] SΣC0..1CodeableConceptActual result
Slice: Unordered, Closed by type:$this
.... value[x]:valueCodeableConcept ΣC0..1CodeableConceptIndeterminate | No call | Present | Absent.
Binding: LOINC Answer List LL1971-2 (required)
... dataAbsentReason SC0..1CodeableConceptWhy the result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

... method S0..1CodeableConceptSequencing | SNP array | PCR | Computational analysis | ...
Binding: LOINC Answer List LL4048-6 (extensible)
... specimen S0..1Reference(Human Specimen Profile)Specimen used for this observation
... referenceRange C0..*BackboneElementNot used in this profile
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
... hasMember Σ0..*Reference(Observation | QuestionnaireResponse | MolecularSequence)Not used in this profile
... Slices for component SΣ0..*BackboneElementComponent results
Slice: Unordered, Open by pattern:code
.... component:All Slices Content/Rules for all slices
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.

.... component:conclusion-string Σ0..1BackboneElementClinical Conclusion
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptconclusion-string
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: conclusion-string
.... component:gene-studied SΣ0..*BackboneElementGene Studied
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code SΣ1..1CodeableConcept48018-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48018-6
..... value[x] SΣ1..1CodeableConceptThe HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used.
Binding: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible)
.... component:cytogenetic-location SΣ0..*BackboneElementCytogenetic (Chromosome) Location
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code SΣ1..1CodeableConcept48001-2
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48001-2
..... value[x] SΣ1..1CodeableConceptExample: 1q21.1
.... component:reference-sequence-assembly Σ0..*BackboneElementHuman Reference Sequence Assembly
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConcept62374-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 62374-4
..... value[x] Σ1..1CodeableConceptGRCh37 | GRCh38 | ...
Binding: LOINC Answer List LL1040-6 (extensible)
.... component:coding-hgvs Σ0..1BackboneElementCoding (cDNA) Change - cHGVS
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConcept48004-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48004-6
..... value[x] Σ1..1CodeableConceptA valid HGVS-formatted 'c.' string, e.g. NM_005228.5:c.2369C>T.
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
.... component:genomic-hgvs SΣ0..1BackboneElementGenomic (gDNA) Change - gHGVS
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code SΣ1..1CodeableConcept81290-9
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81290-9
..... value[x] SΣ1..1CodeableConceptA valid HGVS-formatted 'g.' string, e.g. NC_000016.9:g.2124200_2138612dup
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
.... component:cytogenomic-nomenclature SΣ0..1BackboneElementCytogenomic Nomenclature (ISCN)
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code SΣ1..1CodeableConcept81291-7
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81291-7
..... value[x] SΣ1..1CodeableConceptActual component result
Binding: (unbound) (example): Binding not yet defined

.... component:genomic-ref-seq Σ0..1BackboneElementGenomic Reference Sequence
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConcept48013-7
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48013-7
..... value[x] Σ1..1CodeableConceptVersioned genomic reference sequence identifier
Binding: (unbound) (example): Multiple bindings acceptable (NCBI or LRG)

.... component:transcript-ref-seq Σ0..1BackboneElementReference Transcript
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConcept51958-7
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 51958-7
..... value[x] Σ1..1CodeableConceptVersioned transcript reference sequence identifier
Binding: (unbound) (example): Multiple bindings acceptable (NCBI or LRG)

.... component:exact-start-end Σ0..1BackboneElementExact Start-End
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConcept81254-5
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81254-5
.... component:inner-start-end Σ0..1BackboneElementInner Start-End
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConcept81302-2
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81302-2
.... component:outer-start-end Σ0..1BackboneElementOuter Start-End
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConcept81301-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81301-4
.... component:coordinate-system Σ0..1BackboneElementCoordinate System
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConcept92822-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 92822-6
..... value[x] Σ1..1CodeableConcept0-based interval counting | 0-based character counting | 1-based character counting
Binding: LOINC Answer List LL5323-2 (extensible)
.... component:ref-allele Σ0..1BackboneElementGenomic Ref Allele
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConcept69547-8
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 69547-8
.... component:alt-allele Σ0..1BackboneElementGenomic Alt Allele
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConcept69551-0
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 69551-0
.... component:coding-change-type SΣ0..1BackboneElementCoding DNA Change Type
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code SΣ1..1CodeableConcept48019-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48019-4
..... value[x] SΣ1..1CodeableConceptdeletion | insertion | delins | SNV | copy_number_gain | copy_number_loss | ... (many)
Binding: DNA Change Type (extensible): Concepts in sequence ontology under SO:0002072

.... component:genomic-source-class SΣ0..1BackboneElementGenomic Source Class
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code SΣ1..1CodeableConcept48002-0
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48002-0
..... value[x] SΣ1..1CodeableConceptGermline | Somatic | Fetal | Likely germline | Likely somatic | Likely fetal | Unknown genomic origin | De novo
Binding: LOINC Answer List LL378-1 (extensible)
.... component:sample-allelic-frequency SΣ0..1BackboneElementSample Allelic Frequency
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code SΣ1..1CodeableConcept81258-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81258-6
..... value[x] SΣ0..1QuantityRelative frequency in the sample
...... comparator ?!Σ0..1code< | <= | >= | > - how to understand the value
Binding: QuantityComparator (required): How the Quantity should be understood and represented.

.... component:allelic-read-depth Σ0..1BackboneElementAllelic Read Depth
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConcept82121-5
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 82121-5
.... component:allelic-state SΣ0..1BackboneElementAllelic State
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code SΣ1..1CodeableConcept53034-5
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 53034-5
..... value[x] SΣ1..1CodeableConceptHeteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous
Binding: LOINC Answer List LL381-5 (extensible)
.... component:variant-inheritance Σ0..1BackboneElementVariant Inheritance
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptvariant-inheritance
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: variant-inheritance
..... value[x] Σ1..1CodeableConceptMaternal | Paternal | Unknown
Binding: Variant Inheritances (extensible)
.... component:variation-code SΣ0..*BackboneElementVariation Code
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code SΣ1..1CodeableConcept81252-9
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81252-9
..... value[x] SΣ1..1CodeableConceptClinVar ID or similar
Binding: (unbound) (example): Multiple bindings acceptable

.... component:chromosome-identifier Σ0..*BackboneElementChromosome Identifier
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConcept48000-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48000-4
..... value[x] Σ1..1CodeableConceptChromosome 1 | Chromosome 2 | ... | Chromosome 22 | Chromosome X | Chromosome Y
Binding: LOINC Answer List LL2938-0 (required)
.... component:protein-hgvs SΣ0..1BackboneElementProtein (Amino Acid) Change - pHGVS
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code SΣ1..1CodeableConcept48005-3
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48005-3
..... value[x] SΣ1..1CodeableConceptA valid HGVS-formatted 'p.' string, e.g. NP_000050.2:p.(Asn1836Lys)
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
.... component:amino-acid-change-type SΣ0..1BackboneElementAmino Acid Change Type
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code SΣ1..1CodeableConcept48006-1
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48006-1
..... value[x] SΣ1..1CodeableConceptWild type | Deletion | Duplication | Frameshift | Initiating Methionine | Insertion | Insertion and Deletion | Missense | Nonsense | Silent
Binding: LOINC Answer List LL380-7 (extensible)
.... component:molecular-consequence SΣ0..1BackboneElementMolecular Consequence
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code SΣ1..1CodeableConceptmolecular-consequence
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: molecular-consequence
..... value[x] SΣ1..1CodeableConceptstop_lost | stop_gained | inframe_insertion | frameshift_variant | ... (many)
Binding: Molecular Consequence (extensible): Concepts in sequence ontology under SO:0001537.

.... component:copy-number SΣ0..1BackboneElementGenomic Structural Variant Copy Number
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code SΣ1..1CodeableConcept82155-3
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 82155-3
..... value[x] SΣC0..1QuantityActual component result
.... component:variant-confidence-status Σ0..1BackboneElementVariant Confidence Status
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptvariant-confidence-status
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: variant-confidence-status
..... value[x] Σ1..1CodeableConceptHigh | Intermediate | Low
Binding: Variant Confidence Status (required)

doco Documentation for this format

Terminology Bindings

PathConformanceValueSet / Code
Observation.statusrequiredObservationStatus
Observation.categorypreferredObservationCategoryCodes
Observation.category:labCategorypreferredPattern: laboratory
Observation.codeexamplePattern: LOINC code 69548-6
Observation.value[x]:valueCodeableConceptrequiredLOINC LL1971-2
Observation.dataAbsentReasonextensibleDataAbsentReason
Observation.methodextensibleLOINC LL4048-6
Observation.component.codeexampleLOINCCodes (a valid code from LOINC)
Observation.component:conclusion-string.codeexamplePattern: conclusion-string
Observation.component:gene-studied.codeexamplePattern: LOINC code 48018-6
Observation.component:gene-studied.value[x]extensibleHGNCVS
Observation.component:cytogenetic-location.codeexamplePattern: LOINC code 48001-2
Observation.component:reference-sequence-assembly.codeexamplePattern: LOINC code 62374-4
Observation.component:reference-sequence-assembly.value[x]extensibleLOINC LL1040-6
Observation.component:coding-hgvs.codeexamplePattern: LOINC code 48004-6
Observation.component:coding-hgvs.value[x]requiredHGVSVS
Observation.component:genomic-hgvs.codeexamplePattern: LOINC code 81290-9
Observation.component:genomic-hgvs.value[x]requiredHGVSVS
Observation.component:cytogenomic-nomenclature.codeexamplePattern: LOINC code 81291-7
Observation.component:cytogenomic-nomenclature.value[x]example
Observation.component:genomic-ref-seq.codeexamplePattern: LOINC code 48013-7
Observation.component:genomic-ref-seq.value[x]example
Observation.component:transcript-ref-seq.codeexamplePattern: LOINC code 51958-7
Observation.component:transcript-ref-seq.value[x]example
Observation.component:exact-start-end.codeexamplePattern: LOINC code 81254-5
Observation.component:inner-start-end.codeexamplePattern: LOINC code 81302-2
Observation.component:outer-start-end.codeexamplePattern: LOINC code 81301-4
Observation.component:coordinate-system.codeexamplePattern: LOINC code 92822-6
Observation.component:coordinate-system.value[x]extensibleLOINC LL5323-2
Observation.component:ref-allele.codeexamplePattern: LOINC code 69547-8
Observation.component:alt-allele.codeexamplePattern: LOINC code 69551-0
Observation.component:coding-change-type.codeexamplePattern: LOINC code 48019-4
Observation.component:coding-change-type.value[x]extensibleDNAChangeTypeVS
Observation.component:genomic-source-class.codeexamplePattern: LOINC code 48002-0
Observation.component:genomic-source-class.value[x]extensibleLOINC LL378-1
Observation.component:sample-allelic-frequency.codeexamplePattern: LOINC code 81258-6
Observation.component:sample-allelic-frequency.value[x].comparatorrequiredQuantityComparator
Observation.component:allelic-read-depth.codeexamplePattern: LOINC code 82121-5
Observation.component:allelic-state.codeexamplePattern: LOINC code 53034-5
Observation.component:allelic-state.value[x]extensibleLOINC LL381-5
Observation.component:variant-inheritance.codeexamplePattern: variant-inheritance
Observation.component:variant-inheritance.value[x]extensibleVariantInheritanceVS
Observation.component:variation-code.codeexamplePattern: LOINC code 81252-9
Observation.component:variation-code.value[x]example
Observation.component:chromosome-identifier.codeexamplePattern: LOINC code 48000-4
Observation.component:chromosome-identifier.value[x]requiredLOINC LL2938-0
Observation.component:protein-hgvs.codeexamplePattern: LOINC code 48005-3
Observation.component:protein-hgvs.value[x]requiredHGVSVS
Observation.component:amino-acid-change-type.codeexamplePattern: LOINC code 48006-1
Observation.component:amino-acid-change-type.value[x]extensibleLOINC LL380-7
Observation.component:molecular-consequence.codeexamplePattern: molecular-consequence
Observation.component:molecular-consequence.value[x]extensibleMolecularConsequenceVS
Observation.component:copy-number.codeexamplePattern: LOINC code 82155-3
Observation.component:variant-confidence-status.codeexamplePattern: variant-confidence-status
Observation.component:variant-confidence-status.value[x]requiredVariantConfidenceStatusVS
NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation C0..*VariantVariant
... id Σ0..1idLogical id of this artifact
... meta Σ0..1MetaMetadata about the resource
... implicitRules ?!Σ0..1uriA set of rules under which this content was created
... language 0..1codeLanguage of the resource content
Binding: CommonLanguages (preferred): A human language.

Additional BindingsPurpose
AllLanguagesMax Binding
... text 0..1NarrativeText summary of the resource, for human interpretation
... contained 0..*ResourceContained, inline Resources
... Slices for extension 0..*ExtensionExtension
Slice: Unordered, Open by value:url
... secondary-finding 0..1CodeableConceptSecondary findings are genetic test results that provide information about variants in a gene unrelated to the primary purpose for the testing, most often discovered when [Whole Exome Sequencing (WES)](https://en.wikipedia.org/wiki/Exome_sequencing) or [Whole Genome Sequencing (WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) is performed. This extension should be used to denote when a genetic finding is being shared as a secondary finding, and ideally refer to a corresponding guideline or policy statement. For more detail, please see: https://ghr.nlm.nih.gov/primer/testing/secondaryfindings
URL: http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding
Binding: GeneticObservationSecondaryFindings (extensible): Codes to denote a guideline or policy statement when a genetic test result is being shared as a secondary finding.


... body-structure 0..1Reference(BodyStructure)Target anatomic location or structure
URL: http://hl7.org/fhir/StructureDefinition/bodySite
... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
... identifier Σ0..*IdentifierBusiness Identifier for observation
... basedOn Σ0..*Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest)Fulfills plan, proposal or order
... partOf Σ0..*Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy)Part of referenced event
... status ?!SΣ1..1coderegistered | preliminary | final | amended +
Binding: ObservationStatus (required): Codes providing the status of an observation.

... Slices for category S1..*CodeableConceptClassification of type of observation
Slice: Unordered, Open by value:coding
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.


.... category:labCategory 1..1CodeableConceptClassification of type of observation
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.



Required Pattern: At least the following
..... id0..1stringUnique id for inter-element referencing
..... extension0..*ExtensionAdditional content defined by implementations
..... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... system1..1uriIdentity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
...... version0..1stringVersion of the system - if relevant
...... code1..1codeSymbol in syntax defined by the system
Fixed Value: laboratory
...... display0..1stringRepresentation defined by the system
...... userSelected0..1booleanIf this coding was chosen directly by the user
..... text0..1stringPlain text representation of the concept
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
..... coding Σ1..1CodingCode defined by a terminology system

Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... system1..1uriIdentity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
...... version0..1stringVersion of the system - if relevant
...... code1..1codeSymbol in syntax defined by the system
Fixed Value: laboratory
...... display0..1stringRepresentation defined by the system
...... userSelected0..1booleanIf this coding was chosen directly by the user
..... text Σ0..1stringPlain text representation of the concept
... code SΣ1..1CodeableConcept69548-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
.... id0..1stringUnique id for inter-element referencing
.... extension0..*ExtensionAdditional content defined by implementations
.... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
..... id0..1stringUnique id for inter-element referencing
..... extension0..*ExtensionAdditional content defined by implementations
..... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
..... version0..1stringVersion of the system - if relevant
..... code1..1codeSymbol in syntax defined by the system
Fixed Value: 69548-6
..... display0..1stringRepresentation defined by the system
..... userSelected0..1booleanIf this coding was chosen directly by the user
.... text0..1stringPlain text representation of the concept
... subject SΣ0..1Reference(Cancer Patient Profile)Who and/or what the observation is about
... focus ΣTU0..*Reference(Resource)What the observation is about, when it is not about the subject of record
... encounter Σ0..1Reference(Encounter)Healthcare event during which this observation is made
... Slices for effective[x] SΣ0..1Clinically relevant time/time-period for observation
Slice: Unordered, Open by type:$this
.... effectiveDateTimedateTime
.... effectivePeriodPeriod
.... effectiveTimingTiming
.... effectiveInstantinstant
.... effective[x]:effectiveDateTime SΣ0..1dateTimeClinically relevant time/time-period for observation
... issued Σ0..1instantDate/Time this version was made available
... performer Σ0..*Reference(Practitioner | PractitionerRole | Organization | CareTeam | Patient | RelatedPerson)Who is responsible for the observation
... Slices for value[x] SΣC0..1CodeableConceptActual result
Slice: Unordered, Closed by type:$this
.... value[x]:valueCodeableConcept ΣC0..1CodeableConceptIndeterminate | No call | Present | Absent.
Binding: LOINC Answer List LL1971-2 (required)
... dataAbsentReason SC0..1CodeableConceptWhy the result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


... note 0..*CodedAnnotationComments about the Observation that also contain a coded type
... bodySite 0..1CodeableConceptObserved body part
Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality.

... method S0..1CodeableConceptSequencing | SNP array | PCR | Computational analysis | ...
Binding: LOINC Answer List LL4048-6 (extensible)
... specimen S0..1Reference(Human Specimen Profile)Specimen used for this observation
... device 0..1Reference(Device | DeviceMetric)(Measurement) Device
... referenceRange C0..*BackboneElementNot used in this profile
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... low C0..1SimpleQuantityLow Range, if relevant
.... high C0..1SimpleQuantityHigh Range, if relevant
.... type 0..1CodeableConceptReference range qualifier
Binding: ObservationReferenceRangeMeaningCodes (preferred): Code for the meaning of a reference range.

.... appliesTo 0..*CodeableConceptReference range population
Binding: ObservationReferenceRangeAppliesToCodes (example): Codes identifying the population the reference range applies to.


.... age 0..1RangeApplicable age range, if relevant
.... text 0..1stringText based reference range in an observation
... hasMember Σ0..*Reference(Observation | QuestionnaireResponse | MolecularSequence)Not used in this profile
... derivedFrom Σ0..*Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence)Related measurements the observation is made from
... Slices for component SΣ0..*BackboneElementComponent results
Slice: Unordered, Open by pattern:code
.... component:All Slices Content/Rules for all slices
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.

..... value[x] Σ0..1Actual component result
...... valueQuantityQuantity
...... valueCodeableConceptCodeableConcept
...... valueStringstring
...... valueBooleanboolean
...... valueIntegerinteger
...... valueRangeRange
...... valueRatioRatio
...... valueSampledDataSampledData
...... valueTimetime
...... valueDateTimedateTime
...... valuePeriodPeriod
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:conclusion-string Σ0..1BackboneElementClinical Conclusion
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptconclusion-string
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: conclusion-string
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ0..1stringSummary conclusion (interpretation/impression)
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:gene-studied SΣ0..*BackboneElementGene Studied
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code SΣ1..1CodeableConcept48018-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48018-6
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] SΣ1..1CodeableConceptThe HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used.
Binding: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible)
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:cytogenetic-location SΣ0..*BackboneElementCytogenetic (Chromosome) Location
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code SΣ1..1CodeableConcept48001-2
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48001-2
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] SΣ1..1CodeableConceptExample: 1q21.1
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:reference-sequence-assembly Σ0..*BackboneElementHuman Reference Sequence Assembly
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConcept62374-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 62374-4
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1CodeableConceptGRCh37 | GRCh38 | ...
Binding: LOINC Answer List LL1040-6 (extensible)
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:coding-hgvs Σ0..1BackboneElementCoding (cDNA) Change - cHGVS
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConcept48004-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48004-6
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1CodeableConceptA valid HGVS-formatted 'c.' string, e.g. NM_005228.5:c.2369C>T.
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:genomic-hgvs SΣ0..1BackboneElementGenomic (gDNA) Change - gHGVS
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code SΣ1..1CodeableConcept81290-9
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81290-9
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] SΣ1..1CodeableConceptA valid HGVS-formatted 'g.' string, e.g. NC_000016.9:g.2124200_2138612dup
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:cytogenomic-nomenclature SΣ0..1BackboneElementCytogenomic Nomenclature (ISCN)
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code SΣ1..1CodeableConcept81291-7
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81291-7
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] SΣ1..1CodeableConceptActual component result
Binding: (unbound) (example): Binding not yet defined

..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:genomic-ref-seq Σ0..1BackboneElementGenomic Reference Sequence
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConcept48013-7
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48013-7
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1CodeableConceptVersioned genomic reference sequence identifier
Binding: (unbound) (example): Multiple bindings acceptable (NCBI or LRG)

..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:transcript-ref-seq Σ0..1BackboneElementReference Transcript
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConcept51958-7
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 51958-7
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1CodeableConceptVersioned transcript reference sequence identifier
Binding: (unbound) (example): Multiple bindings acceptable (NCBI or LRG)

..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:exact-start-end Σ0..1BackboneElementExact Start-End
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConcept81254-5
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81254-5
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ0..1RangeRange in question. 'High' can be omitted for single nucleotide variants.
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:inner-start-end Σ0..1BackboneElementInner Start-End
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConcept81302-2
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81302-2
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ0..1RangeImprecise variant inner-bounding range
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:outer-start-end Σ0..1BackboneElementOuter Start-End
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConcept81301-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81301-4
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ0..1RangeImprecise variant outer-bounding range
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:coordinate-system Σ0..1BackboneElementCoordinate System
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConcept92822-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 92822-6
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1CodeableConcept0-based interval counting | 0-based character counting | 1-based character counting
Binding: LOINC Answer List LL5323-2 (extensible)
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:ref-allele Σ0..1BackboneElementGenomic Ref Allele
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConcept69547-8
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 69547-8
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ0..1stringNormalized string per the VCF format.
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:alt-allele Σ0..1BackboneElementGenomic Alt Allele
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConcept69551-0
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 69551-0
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ0..1stringNormalized string per the VCF format.
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:coding-change-type SΣ0..1BackboneElementCoding DNA Change Type
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code SΣ1..1CodeableConcept48019-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48019-4
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] SΣ1..1CodeableConceptdeletion | insertion | delins | SNV | copy_number_gain | copy_number_loss | ... (many)
Binding: DNA Change Type (extensible): Concepts in sequence ontology under SO:0002072

..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:genomic-source-class SΣ0..1BackboneElementGenomic Source Class
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code SΣ1..1CodeableConcept48002-0
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48002-0
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] SΣ1..1CodeableConceptGermline | Somatic | Fetal | Likely germline | Likely somatic | Likely fetal | Unknown genomic origin | De novo
Binding: LOINC Answer List LL378-1 (extensible)
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:sample-allelic-frequency SΣ0..1BackboneElementSample Allelic Frequency
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code SΣ1..1CodeableConcept81258-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81258-6
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] SΣ0..1QuantityRelative frequency in the sample
...... id 0..1stringUnique id for inter-element referencing
...... extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
...... value Σ0..1decimalNumerical value (with implicit precision)
...... comparator ?!Σ0..1code< | <= | >= | > - how to understand the value
Binding: QuantityComparator (required): How the Quantity should be understood and represented.

...... unit Σ0..1stringUnit representation
...... system ΣC0..1uriSystem that defines coded unit form
Required Pattern: http://unitsofmeasure.org
...... code Σ0..1codeCoded form of the unit
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:allelic-read-depth Σ0..1BackboneElementAllelic Read Depth
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConcept82121-5
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 82121-5
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ0..1QuantityUnfiltered count of supporting reads
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:allelic-state SΣ0..1BackboneElementAllelic State
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code SΣ1..1CodeableConcept53034-5
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 53034-5
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] SΣ1..1CodeableConceptHeteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous
Binding: LOINC Answer List LL381-5 (extensible)
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:variant-inheritance Σ0..1BackboneElementVariant Inheritance
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptvariant-inheritance
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: variant-inheritance
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1CodeableConceptMaternal | Paternal | Unknown
Binding: Variant Inheritances (extensible)
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:variation-code SΣ0..*BackboneElementVariation Code
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code SΣ1..1CodeableConcept81252-9
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81252-9
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] SΣ1..1CodeableConceptClinVar ID or similar
Binding: (unbound) (example): Multiple bindings acceptable

..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:chromosome-identifier Σ0..*BackboneElementChromosome Identifier
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConcept48000-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48000-4
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1CodeableConceptChromosome 1 | Chromosome 2 | ... | Chromosome 22 | Chromosome X | Chromosome Y
Binding: LOINC Answer List LL2938-0 (required)
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:protein-hgvs SΣ0..1BackboneElementProtein (Amino Acid) Change - pHGVS
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code SΣ1..1CodeableConcept48005-3
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48005-3
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] SΣ1..1CodeableConceptA valid HGVS-formatted 'p.' string, e.g. NP_000050.2:p.(Asn1836Lys)
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:amino-acid-change-type SΣ0..1BackboneElementAmino Acid Change Type
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code SΣ1..1CodeableConcept48006-1
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48006-1
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] SΣ1..1CodeableConceptWild type | Deletion | Duplication | Frameshift | Initiating Methionine | Insertion | Insertion and Deletion | Missense | Nonsense | Silent
Binding: LOINC Answer List LL380-7 (extensible)
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:molecular-consequence SΣ0..1BackboneElementMolecular Consequence
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code SΣ1..1CodeableConceptmolecular-consequence
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: molecular-consequence
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] SΣ1..1CodeableConceptstop_lost | stop_gained | inframe_insertion | frameshift_variant | ... (many)
Binding: Molecular Consequence (extensible): Concepts in sequence ontology under SO:0001537.

..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:copy-number SΣ0..1BackboneElementGenomic Structural Variant Copy Number
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code SΣ1..1CodeableConcept82155-3
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 82155-3
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] SΣC0..1QuantityActual component result
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:variant-confidence-status Σ0..1BackboneElementVariant Confidence Status
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptvariant-confidence-status
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: variant-confidence-status
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1CodeableConceptHigh | Intermediate | Low
Binding: Variant Confidence Status (required)
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result

doco Documentation for this format

Terminology Bindings

PathConformanceValueSet / Code
Observation.languagepreferredCommonLanguages
Additional Bindings Purpose
AllLanguages Max Binding
Observation.statusrequiredObservationStatus
Observation.categorypreferredObservationCategoryCodes
Observation.category:labCategorypreferredPattern: laboratory
Observation.codeexamplePattern: LOINC code 69548-6
Observation.value[x]:valueCodeableConceptrequiredLOINC LL1971-2
Observation.dataAbsentReasonextensibleDataAbsentReason
Observation.interpretationextensibleObservationInterpretationCodes
Observation.bodySiteexampleSNOMEDCTBodyStructures
Observation.methodextensibleLOINC LL4048-6
Observation.referenceRange.typepreferredObservationReferenceRangeMeaningCodes
Observation.referenceRange.appliesToexampleObservationReferenceRangeAppliesToCodes
Observation.component.codeexampleLOINCCodes (a valid code from LOINC)
Observation.component.dataAbsentReasonextensibleDataAbsentReason
Observation.component.interpretationextensibleObservationInterpretationCodes
Observation.component:conclusion-string.codeexamplePattern: conclusion-string
Observation.component:conclusion-string.dataAbsentReasonextensibleDataAbsentReason
Observation.component:conclusion-string.interpretationextensibleObservationInterpretationCodes
Observation.component:gene-studied.codeexamplePattern: LOINC code 48018-6
Observation.component:gene-studied.value[x]extensibleHGNCVS
Observation.component:gene-studied.dataAbsentReasonextensibleDataAbsentReason
Observation.component:gene-studied.interpretationextensibleObservationInterpretationCodes
Observation.component:cytogenetic-location.codeexamplePattern: LOINC code 48001-2
Observation.component:cytogenetic-location.dataAbsentReasonextensibleDataAbsentReason
Observation.component:cytogenetic-location.interpretationextensibleObservationInterpretationCodes
Observation.component:reference-sequence-assembly.codeexamplePattern: LOINC code 62374-4
Observation.component:reference-sequence-assembly.value[x]extensibleLOINC LL1040-6
Observation.component:reference-sequence-assembly.dataAbsentReasonextensibleDataAbsentReason
Observation.component:reference-sequence-assembly.interpretationextensibleObservationInterpretationCodes
Observation.component:coding-hgvs.codeexamplePattern: LOINC code 48004-6
Observation.component:coding-hgvs.value[x]requiredHGVSVS
Observation.component:coding-hgvs.dataAbsentReasonextensibleDataAbsentReason
Observation.component:coding-hgvs.interpretationextensibleObservationInterpretationCodes
Observation.component:genomic-hgvs.codeexamplePattern: LOINC code 81290-9
Observation.component:genomic-hgvs.value[x]requiredHGVSVS
Observation.component:genomic-hgvs.dataAbsentReasonextensibleDataAbsentReason
Observation.component:genomic-hgvs.interpretationextensibleObservationInterpretationCodes
Observation.component:cytogenomic-nomenclature.codeexamplePattern: LOINC code 81291-7
Observation.component:cytogenomic-nomenclature.value[x]example
Observation.component:cytogenomic-nomenclature.dataAbsentReasonextensibleDataAbsentReason
Observation.component:cytogenomic-nomenclature.interpretationextensibleObservationInterpretationCodes
Observation.component:genomic-ref-seq.codeexamplePattern: LOINC code 48013-7
Observation.component:genomic-ref-seq.value[x]example
Observation.component:genomic-ref-seq.dataAbsentReasonextensibleDataAbsentReason
Observation.component:genomic-ref-seq.interpretationextensibleObservationInterpretationCodes
Observation.component:transcript-ref-seq.codeexamplePattern: LOINC code 51958-7
Observation.component:transcript-ref-seq.value[x]example
Observation.component:transcript-ref-seq.dataAbsentReasonextensibleDataAbsentReason
Observation.component:transcript-ref-seq.interpretationextensibleObservationInterpretationCodes
Observation.component:exact-start-end.codeexamplePattern: LOINC code 81254-5
Observation.component:exact-start-end.dataAbsentReasonextensibleDataAbsentReason
Observation.component:exact-start-end.interpretationextensibleObservationInterpretationCodes
Observation.component:inner-start-end.codeexamplePattern: LOINC code 81302-2
Observation.component:inner-start-end.dataAbsentReasonextensibleDataAbsentReason
Observation.component:inner-start-end.interpretationextensibleObservationInterpretationCodes
Observation.component:outer-start-end.codeexamplePattern: LOINC code 81301-4
Observation.component:outer-start-end.dataAbsentReasonextensibleDataAbsentReason
Observation.component:outer-start-end.interpretationextensibleObservationInterpretationCodes
Observation.component:coordinate-system.codeexamplePattern: LOINC code 92822-6
Observation.component:coordinate-system.value[x]extensibleLOINC LL5323-2
Observation.component:coordinate-system.dataAbsentReasonextensibleDataAbsentReason
Observation.component:coordinate-system.interpretationextensibleObservationInterpretationCodes
Observation.component:ref-allele.codeexamplePattern: LOINC code 69547-8
Observation.component:ref-allele.dataAbsentReasonextensibleDataAbsentReason
Observation.component:ref-allele.interpretationextensibleObservationInterpretationCodes
Observation.component:alt-allele.codeexamplePattern: LOINC code 69551-0
Observation.component:alt-allele.dataAbsentReasonextensibleDataAbsentReason
Observation.component:alt-allele.interpretationextensibleObservationInterpretationCodes
Observation.component:coding-change-type.codeexamplePattern: LOINC code 48019-4
Observation.component:coding-change-type.value[x]extensibleDNAChangeTypeVS
Observation.component:coding-change-type.dataAbsentReasonextensibleDataAbsentReason
Observation.component:coding-change-type.interpretationextensibleObservationInterpretationCodes
Observation.component:genomic-source-class.codeexamplePattern: LOINC code 48002-0
Observation.component:genomic-source-class.value[x]extensibleLOINC LL378-1
Observation.component:genomic-source-class.dataAbsentReasonextensibleDataAbsentReason
Observation.component:genomic-source-class.interpretationextensibleObservationInterpretationCodes
Observation.component:sample-allelic-frequency.codeexamplePattern: LOINC code 81258-6
Observation.component:sample-allelic-frequency.value[x].comparatorrequiredQuantityComparator
Observation.component:sample-allelic-frequency.dataAbsentReasonextensibleDataAbsentReason
Observation.component:sample-allelic-frequency.interpretationextensibleObservationInterpretationCodes
Observation.component:allelic-read-depth.codeexamplePattern: LOINC code 82121-5
Observation.component:allelic-read-depth.dataAbsentReasonextensibleDataAbsentReason
Observation.component:allelic-read-depth.interpretationextensibleObservationInterpretationCodes
Observation.component:allelic-state.codeexamplePattern: LOINC code 53034-5
Observation.component:allelic-state.value[x]extensibleLOINC LL381-5
Observation.component:allelic-state.dataAbsentReasonextensibleDataAbsentReason
Observation.component:allelic-state.interpretationextensibleObservationInterpretationCodes
Observation.component:variant-inheritance.codeexamplePattern: variant-inheritance
Observation.component:variant-inheritance.value[x]extensibleVariantInheritanceVS
Observation.component:variant-inheritance.dataAbsentReasonextensibleDataAbsentReason
Observation.component:variant-inheritance.interpretationextensibleObservationInterpretationCodes
Observation.component:variation-code.codeexamplePattern: LOINC code 81252-9
Observation.component:variation-code.value[x]example
Observation.component:variation-code.dataAbsentReasonextensibleDataAbsentReason
Observation.component:variation-code.interpretationextensibleObservationInterpretationCodes
Observation.component:chromosome-identifier.codeexamplePattern: LOINC code 48000-4
Observation.component:chromosome-identifier.value[x]requiredLOINC LL2938-0
Observation.component:chromosome-identifier.dataAbsentReasonextensibleDataAbsentReason
Observation.component:chromosome-identifier.interpretationextensibleObservationInterpretationCodes
Observation.component:protein-hgvs.codeexamplePattern: LOINC code 48005-3
Observation.component:protein-hgvs.value[x]requiredHGVSVS
Observation.component:protein-hgvs.dataAbsentReasonextensibleDataAbsentReason
Observation.component:protein-hgvs.interpretationextensibleObservationInterpretationCodes
Observation.component:amino-acid-change-type.codeexamplePattern: LOINC code 48006-1
Observation.component:amino-acid-change-type.value[x]extensibleLOINC LL380-7
Observation.component:amino-acid-change-type.dataAbsentReasonextensibleDataAbsentReason
Observation.component:amino-acid-change-type.interpretationextensibleObservationInterpretationCodes
Observation.component:molecular-consequence.codeexamplePattern: molecular-consequence
Observation.component:molecular-consequence.value[x]extensibleMolecularConsequenceVS
Observation.component:molecular-consequence.dataAbsentReasonextensibleDataAbsentReason
Observation.component:molecular-consequence.interpretationextensibleObservationInterpretationCodes
Observation.component:copy-number.codeexamplePattern: LOINC code 82155-3
Observation.component:copy-number.dataAbsentReasonextensibleDataAbsentReason
Observation.component:copy-number.interpretationextensibleObservationInterpretationCodes
Observation.component:variant-confidence-status.codeexamplePattern: variant-confidence-status
Observation.component:variant-confidence-status.value[x]requiredVariantConfidenceStatusVS
Observation.component:variant-confidence-status.dataAbsentReasonextensibleDataAbsentReason
Observation.component:variant-confidence-status.interpretationextensibleObservationInterpretationCodes

This structure is derived from Variant

Summary

Must-Support: 50 elements

Structures

This structure refers to these other structures:

Slices

This structure defines the following Slices:

  • The element Observation.effective[x] is sliced based on the value of type:$this

Maturity: 1

Differential View

This structure is derived from Variant

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation 0..*VariantVariant
... status S1..1coderegistered | preliminary | final | amended +
... category S1..*CodeableConceptClassification of type of observation
... category:labCategory 1..1CodeableConceptClassification of type of observation
Required Pattern: At least the following
.... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
..... system1..1uriIdentity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
..... code1..1codeSymbol in syntax defined by the system
Fixed Value: laboratory
.... coding 1..1CodingCode defined by a terminology system
... subject S0..1Reference(Cancer Patient Profile)Who and/or what the observation is about
... Slices for effective[x] S0..1dateTime, Period, Timing, instantClinically relevant time/time-period for observation
Slice: Unordered, Open by type:$this
.... effective[x]:effectiveDateTime S0..1dateTimeClinically relevant time/time-period for observation
... value[x] S0..1CodeableConceptActual result
... dataAbsentReason S0..1CodeableConceptWhy the result is missing
... method S0..1CodeableConceptSequencing | SNP array | PCR | Computational analysis | ...
... specimen S0..1Reference(Human Specimen Profile)Specimen used for this observation
... referenceRange 0..*BackboneElementNot used in this profile
... hasMember 0..*Reference(Observation | QuestionnaireResponse | MolecularSequence)Not used in this profile
... component S0..*BackboneElementComponent results
... component:gene-studied S0..*BackboneElementGene Studied
.... code S1..1CodeableConcept48018-6
.... value[x] S1..1CodeableConceptThe HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used.
... component:cytogenetic-location S0..*BackboneElementCytogenetic (Chromosome) Location
.... code S1..1CodeableConcept48001-2
.... value[x] S1..1CodeableConceptExample: 1q21.1
... component:genomic-hgvs S0..1BackboneElementGenomic (gDNA) Change - gHGVS
.... code S1..1CodeableConcept81290-9
.... value[x] S1..1CodeableConceptA valid HGVS-formatted 'g.' string, e.g. NC_000016.9:g.2124200_2138612dup
... component:cytogenomic-nomenclature S0..1BackboneElementCytogenomic Nomenclature (ISCN)
.... code S1..1CodeableConcept81291-7
.... value[x] S1..1CodeableConceptActual component result
... component:coding-change-type S0..1BackboneElementCoding DNA Change Type
.... code S1..1CodeableConcept48019-4
.... value[x] S1..1CodeableConceptdeletion | insertion | delins | SNV | copy_number_gain | copy_number_loss | ... (many)
... component:genomic-source-class S0..1BackboneElementGenomic Source Class
.... code S1..1CodeableConcept48002-0
.... value[x] S1..1CodeableConceptGermline | Somatic | Fetal | Likely germline | Likely somatic | Likely fetal | Unknown genomic origin | De novo
... component:sample-allelic-frequency S0..1BackboneElementSample Allelic Frequency
.... code S1..1CodeableConcept81258-6
.... value[x] S0..1QuantityRelative frequency in the sample
... component:allelic-state S0..1BackboneElementAllelic State
.... code S1..1CodeableConcept53034-5
.... value[x] S1..1CodeableConceptHeteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous
... component:variation-code S0..*BackboneElementVariation Code
.... code S1..1CodeableConcept81252-9
.... value[x] S1..1CodeableConceptClinVar ID or similar
... component:protein-hgvs S0..1BackboneElementProtein (Amino Acid) Change - pHGVS
.... code S1..1CodeableConcept48005-3
.... value[x] S1..1CodeableConceptA valid HGVS-formatted 'p.' string, e.g. NP_000050.2:p.(Asn1836Lys)
... component:amino-acid-change-type S0..1BackboneElementAmino Acid Change Type
.... code S1..1CodeableConcept48006-1
.... value[x] S1..1CodeableConceptWild type | Deletion | Duplication | Frameshift | Initiating Methionine | Insertion | Insertion and Deletion | Missense | Nonsense | Silent
... component:molecular-consequence S0..1BackboneElementMolecular Consequence
.... code S1..1CodeableConceptmolecular-consequence
.... value[x] S1..1CodeableConceptstop_lost | stop_gained | inframe_insertion | frameshift_variant | ... (many)
... component:copy-number S0..1BackboneElementGenomic Structural Variant Copy Number
.... code S1..1CodeableConcept82155-3
.... value[x] S0..1QuantityActual component result

doco Documentation for this format

Key Elements View

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation C0..*VariantVariant
... implicitRules ?!Σ0..1uriA set of rules under which this content was created
... secondary-finding 0..1CodeableConceptSecondary findings are genetic test results that provide information about variants in a gene unrelated to the primary purpose for the testing, most often discovered when [Whole Exome Sequencing (WES)](https://en.wikipedia.org/wiki/Exome_sequencing) or [Whole Genome Sequencing (WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) is performed. This extension should be used to denote when a genetic finding is being shared as a secondary finding, and ideally refer to a corresponding guideline or policy statement. For more detail, please see: https://ghr.nlm.nih.gov/primer/testing/secondaryfindings
URL: http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding
Binding: GeneticObservationSecondaryFindings (extensible): Codes to denote a guideline or policy statement when a genetic test result is being shared as a secondary finding.


... body-structure 0..1Reference(BodyStructure)Target anatomic location or structure
URL: http://hl7.org/fhir/StructureDefinition/bodySite
... status ?!SΣ1..1coderegistered | preliminary | final | amended +
Binding: ObservationStatus (required): Codes providing the status of an observation.

... Slices for category S1..*CodeableConceptClassification of type of observation
Slice: Unordered, Open by value:coding
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.


.... category:labCategory 1..1CodeableConceptClassification of type of observation
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.



Required Pattern: At least the following
..... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
...... system1..1uriIdentity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
...... code1..1codeSymbol in syntax defined by the system
Fixed Value: laboratory
..... coding Σ1..1CodingCode defined by a terminology system

Required Pattern: At least the following
...... system1..1uriIdentity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
...... code1..1codeSymbol in syntax defined by the system
Fixed Value: laboratory
... code SΣ1..1CodeableConcept69548-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
.... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
..... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
..... code1..1codeSymbol in syntax defined by the system
Fixed Value: 69548-6
... subject SΣ0..1Reference(Cancer Patient Profile)Who and/or what the observation is about
... Slices for effective[x] SΣ0..1Clinically relevant time/time-period for observation
Slice: Unordered, Open by type:$this
.... effectiveDateTimedateTime
.... effectivePeriodPeriod
.... effectiveTimingTiming
.... effectiveInstantinstant
.... effective[x]:effectiveDateTime SΣ0..1dateTimeClinically relevant time/time-period for observation
... Slices for value[x] SΣC0..1CodeableConceptActual result
Slice: Unordered, Closed by type:$this
.... value[x]:valueCodeableConcept ΣC0..1CodeableConceptIndeterminate | No call | Present | Absent.
Binding: LOINC Answer List LL1971-2 (required)
... dataAbsentReason SC0..1CodeableConceptWhy the result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

... method S0..1CodeableConceptSequencing | SNP array | PCR | Computational analysis | ...
Binding: LOINC Answer List LL4048-6 (extensible)
... specimen S0..1Reference(Human Specimen Profile)Specimen used for this observation
... referenceRange C0..*BackboneElementNot used in this profile
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
... hasMember Σ0..*Reference(Observation | QuestionnaireResponse | MolecularSequence)Not used in this profile
... Slices for component SΣ0..*BackboneElementComponent results
Slice: Unordered, Open by pattern:code
.... component:All Slices Content/Rules for all slices
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.

.... component:conclusion-string Σ0..1BackboneElementClinical Conclusion
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptconclusion-string
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: conclusion-string
.... component:gene-studied SΣ0..*BackboneElementGene Studied
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code SΣ1..1CodeableConcept48018-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48018-6
..... value[x] SΣ1..1CodeableConceptThe HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used.
Binding: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible)
.... component:cytogenetic-location SΣ0..*BackboneElementCytogenetic (Chromosome) Location
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code SΣ1..1CodeableConcept48001-2
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48001-2
..... value[x] SΣ1..1CodeableConceptExample: 1q21.1
.... component:reference-sequence-assembly Σ0..*BackboneElementHuman Reference Sequence Assembly
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConcept62374-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 62374-4
..... value[x] Σ1..1CodeableConceptGRCh37 | GRCh38 | ...
Binding: LOINC Answer List LL1040-6 (extensible)
.... component:coding-hgvs Σ0..1BackboneElementCoding (cDNA) Change - cHGVS
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConcept48004-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48004-6
..... value[x] Σ1..1CodeableConceptA valid HGVS-formatted 'c.' string, e.g. NM_005228.5:c.2369C>T.
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
.... component:genomic-hgvs SΣ0..1BackboneElementGenomic (gDNA) Change - gHGVS
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code SΣ1..1CodeableConcept81290-9
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81290-9
..... value[x] SΣ1..1CodeableConceptA valid HGVS-formatted 'g.' string, e.g. NC_000016.9:g.2124200_2138612dup
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
.... component:cytogenomic-nomenclature SΣ0..1BackboneElementCytogenomic Nomenclature (ISCN)
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code SΣ1..1CodeableConcept81291-7
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81291-7
..... value[x] SΣ1..1CodeableConceptActual component result
Binding: (unbound) (example): Binding not yet defined

.... component:genomic-ref-seq Σ0..1BackboneElementGenomic Reference Sequence
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConcept48013-7
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48013-7
..... value[x] Σ1..1CodeableConceptVersioned genomic reference sequence identifier
Binding: (unbound) (example): Multiple bindings acceptable (NCBI or LRG)

.... component:transcript-ref-seq Σ0..1BackboneElementReference Transcript
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConcept51958-7
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 51958-7
..... value[x] Σ1..1CodeableConceptVersioned transcript reference sequence identifier
Binding: (unbound) (example): Multiple bindings acceptable (NCBI or LRG)

.... component:exact-start-end Σ0..1BackboneElementExact Start-End
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConcept81254-5
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81254-5
.... component:inner-start-end Σ0..1BackboneElementInner Start-End
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConcept81302-2
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81302-2
.... component:outer-start-end Σ0..1BackboneElementOuter Start-End
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConcept81301-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81301-4
.... component:coordinate-system Σ0..1BackboneElementCoordinate System
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConcept92822-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 92822-6
..... value[x] Σ1..1CodeableConcept0-based interval counting | 0-based character counting | 1-based character counting
Binding: LOINC Answer List LL5323-2 (extensible)
.... component:ref-allele Σ0..1BackboneElementGenomic Ref Allele
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConcept69547-8
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 69547-8
.... component:alt-allele Σ0..1BackboneElementGenomic Alt Allele
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConcept69551-0
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 69551-0
.... component:coding-change-type SΣ0..1BackboneElementCoding DNA Change Type
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code SΣ1..1CodeableConcept48019-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48019-4
..... value[x] SΣ1..1CodeableConceptdeletion | insertion | delins | SNV | copy_number_gain | copy_number_loss | ... (many)
Binding: DNA Change Type (extensible): Concepts in sequence ontology under SO:0002072

.... component:genomic-source-class SΣ0..1BackboneElementGenomic Source Class
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code SΣ1..1CodeableConcept48002-0
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48002-0
..... value[x] SΣ1..1CodeableConceptGermline | Somatic | Fetal | Likely germline | Likely somatic | Likely fetal | Unknown genomic origin | De novo
Binding: LOINC Answer List LL378-1 (extensible)
.... component:sample-allelic-frequency SΣ0..1BackboneElementSample Allelic Frequency
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code SΣ1..1CodeableConcept81258-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81258-6
..... value[x] SΣ0..1QuantityRelative frequency in the sample
...... comparator ?!Σ0..1code< | <= | >= | > - how to understand the value
Binding: QuantityComparator (required): How the Quantity should be understood and represented.

.... component:allelic-read-depth Σ0..1BackboneElementAllelic Read Depth
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConcept82121-5
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 82121-5
.... component:allelic-state SΣ0..1BackboneElementAllelic State
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code SΣ1..1CodeableConcept53034-5
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 53034-5
..... value[x] SΣ1..1CodeableConceptHeteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous
Binding: LOINC Answer List LL381-5 (extensible)
.... component:variant-inheritance Σ0..1BackboneElementVariant Inheritance
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptvariant-inheritance
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: variant-inheritance
..... value[x] Σ1..1CodeableConceptMaternal | Paternal | Unknown
Binding: Variant Inheritances (extensible)
.... component:variation-code SΣ0..*BackboneElementVariation Code
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code SΣ1..1CodeableConcept81252-9
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81252-9
..... value[x] SΣ1..1CodeableConceptClinVar ID or similar
Binding: (unbound) (example): Multiple bindings acceptable

.... component:chromosome-identifier Σ0..*BackboneElementChromosome Identifier
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConcept48000-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48000-4
..... value[x] Σ1..1CodeableConceptChromosome 1 | Chromosome 2 | ... | Chromosome 22 | Chromosome X | Chromosome Y
Binding: LOINC Answer List LL2938-0 (required)
.... component:protein-hgvs SΣ0..1BackboneElementProtein (Amino Acid) Change - pHGVS
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code SΣ1..1CodeableConcept48005-3
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48005-3
..... value[x] SΣ1..1CodeableConceptA valid HGVS-formatted 'p.' string, e.g. NP_000050.2:p.(Asn1836Lys)
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
.... component:amino-acid-change-type SΣ0..1BackboneElementAmino Acid Change Type
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code SΣ1..1CodeableConcept48006-1
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48006-1
..... value[x] SΣ1..1CodeableConceptWild type | Deletion | Duplication | Frameshift | Initiating Methionine | Insertion | Insertion and Deletion | Missense | Nonsense | Silent
Binding: LOINC Answer List LL380-7 (extensible)
.... component:molecular-consequence SΣ0..1BackboneElementMolecular Consequence
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code SΣ1..1CodeableConceptmolecular-consequence
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: molecular-consequence
..... value[x] SΣ1..1CodeableConceptstop_lost | stop_gained | inframe_insertion | frameshift_variant | ... (many)
Binding: Molecular Consequence (extensible): Concepts in sequence ontology under SO:0001537.

.... component:copy-number SΣ0..1BackboneElementGenomic Structural Variant Copy Number
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code SΣ1..1CodeableConcept82155-3
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 82155-3
..... value[x] SΣC0..1QuantityActual component result
.... component:variant-confidence-status Σ0..1BackboneElementVariant Confidence Status
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptvariant-confidence-status
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: variant-confidence-status
..... value[x] Σ1..1CodeableConceptHigh | Intermediate | Low
Binding: Variant Confidence Status (required)

doco Documentation for this format

Terminology Bindings

PathConformanceValueSet / Code
Observation.statusrequiredObservationStatus
Observation.categorypreferredObservationCategoryCodes
Observation.category:labCategorypreferredPattern: laboratory
Observation.codeexamplePattern: LOINC code 69548-6
Observation.value[x]:valueCodeableConceptrequiredLOINC LL1971-2
Observation.dataAbsentReasonextensibleDataAbsentReason
Observation.methodextensibleLOINC LL4048-6
Observation.component.codeexampleLOINCCodes (a valid code from LOINC)
Observation.component:conclusion-string.codeexamplePattern: conclusion-string
Observation.component:gene-studied.codeexamplePattern: LOINC code 48018-6
Observation.component:gene-studied.value[x]extensibleHGNCVS
Observation.component:cytogenetic-location.codeexamplePattern: LOINC code 48001-2
Observation.component:reference-sequence-assembly.codeexamplePattern: LOINC code 62374-4
Observation.component:reference-sequence-assembly.value[x]extensibleLOINC LL1040-6
Observation.component:coding-hgvs.codeexamplePattern: LOINC code 48004-6
Observation.component:coding-hgvs.value[x]requiredHGVSVS
Observation.component:genomic-hgvs.codeexamplePattern: LOINC code 81290-9
Observation.component:genomic-hgvs.value[x]requiredHGVSVS
Observation.component:cytogenomic-nomenclature.codeexamplePattern: LOINC code 81291-7
Observation.component:cytogenomic-nomenclature.value[x]example
Observation.component:genomic-ref-seq.codeexamplePattern: LOINC code 48013-7
Observation.component:genomic-ref-seq.value[x]example
Observation.component:transcript-ref-seq.codeexamplePattern: LOINC code 51958-7
Observation.component:transcript-ref-seq.value[x]example
Observation.component:exact-start-end.codeexamplePattern: LOINC code 81254-5
Observation.component:inner-start-end.codeexamplePattern: LOINC code 81302-2
Observation.component:outer-start-end.codeexamplePattern: LOINC code 81301-4
Observation.component:coordinate-system.codeexamplePattern: LOINC code 92822-6
Observation.component:coordinate-system.value[x]extensibleLOINC LL5323-2
Observation.component:ref-allele.codeexamplePattern: LOINC code 69547-8
Observation.component:alt-allele.codeexamplePattern: LOINC code 69551-0
Observation.component:coding-change-type.codeexamplePattern: LOINC code 48019-4
Observation.component:coding-change-type.value[x]extensibleDNAChangeTypeVS
Observation.component:genomic-source-class.codeexamplePattern: LOINC code 48002-0
Observation.component:genomic-source-class.value[x]extensibleLOINC LL378-1
Observation.component:sample-allelic-frequency.codeexamplePattern: LOINC code 81258-6
Observation.component:sample-allelic-frequency.value[x].comparatorrequiredQuantityComparator
Observation.component:allelic-read-depth.codeexamplePattern: LOINC code 82121-5
Observation.component:allelic-state.codeexamplePattern: LOINC code 53034-5
Observation.component:allelic-state.value[x]extensibleLOINC LL381-5
Observation.component:variant-inheritance.codeexamplePattern: variant-inheritance
Observation.component:variant-inheritance.value[x]extensibleVariantInheritanceVS
Observation.component:variation-code.codeexamplePattern: LOINC code 81252-9
Observation.component:variation-code.value[x]example
Observation.component:chromosome-identifier.codeexamplePattern: LOINC code 48000-4
Observation.component:chromosome-identifier.value[x]requiredLOINC LL2938-0
Observation.component:protein-hgvs.codeexamplePattern: LOINC code 48005-3
Observation.component:protein-hgvs.value[x]requiredHGVSVS
Observation.component:amino-acid-change-type.codeexamplePattern: LOINC code 48006-1
Observation.component:amino-acid-change-type.value[x]extensibleLOINC LL380-7
Observation.component:molecular-consequence.codeexamplePattern: molecular-consequence
Observation.component:molecular-consequence.value[x]extensibleMolecularConsequenceVS
Observation.component:copy-number.codeexamplePattern: LOINC code 82155-3
Observation.component:variant-confidence-status.codeexamplePattern: variant-confidence-status
Observation.component:variant-confidence-status.value[x]requiredVariantConfidenceStatusVS

Snapshot View

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation C0..*VariantVariant
... id Σ0..1idLogical id of this artifact
... meta Σ0..1MetaMetadata about the resource
... implicitRules ?!Σ0..1uriA set of rules under which this content was created
... language 0..1codeLanguage of the resource content
Binding: CommonLanguages (preferred): A human language.

Additional BindingsPurpose
AllLanguagesMax Binding
... text 0..1NarrativeText summary of the resource, for human interpretation
... contained 0..*ResourceContained, inline Resources
... Slices for extension 0..*ExtensionExtension
Slice: Unordered, Open by value:url
... secondary-finding 0..1CodeableConceptSecondary findings are genetic test results that provide information about variants in a gene unrelated to the primary purpose for the testing, most often discovered when [Whole Exome Sequencing (WES)](https://en.wikipedia.org/wiki/Exome_sequencing) or [Whole Genome Sequencing (WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) is performed. This extension should be used to denote when a genetic finding is being shared as a secondary finding, and ideally refer to a corresponding guideline or policy statement. For more detail, please see: https://ghr.nlm.nih.gov/primer/testing/secondaryfindings
URL: http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding
Binding: GeneticObservationSecondaryFindings (extensible): Codes to denote a guideline or policy statement when a genetic test result is being shared as a secondary finding.


... body-structure 0..1Reference(BodyStructure)Target anatomic location or structure
URL: http://hl7.org/fhir/StructureDefinition/bodySite
... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
... identifier Σ0..*IdentifierBusiness Identifier for observation
... basedOn Σ0..*Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest)Fulfills plan, proposal or order
... partOf Σ0..*Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy)Part of referenced event
... status ?!SΣ1..1coderegistered | preliminary | final | amended +
Binding: ObservationStatus (required): Codes providing the status of an observation.

... Slices for category S1..*CodeableConceptClassification of type of observation
Slice: Unordered, Open by value:coding
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.


.... category:labCategory 1..1CodeableConceptClassification of type of observation
Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.



Required Pattern: At least the following
..... id0..1stringUnique id for inter-element referencing
..... extension0..*ExtensionAdditional content defined by implementations
..... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... system1..1uriIdentity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
...... version0..1stringVersion of the system - if relevant
...... code1..1codeSymbol in syntax defined by the system
Fixed Value: laboratory
...... display0..1stringRepresentation defined by the system
...... userSelected0..1booleanIf this coding was chosen directly by the user
..... text0..1stringPlain text representation of the concept
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
..... coding Σ1..1CodingCode defined by a terminology system

Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... system1..1uriIdentity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
...... version0..1stringVersion of the system - if relevant
...... code1..1codeSymbol in syntax defined by the system
Fixed Value: laboratory
...... display0..1stringRepresentation defined by the system
...... userSelected0..1booleanIf this coding was chosen directly by the user
..... text Σ0..1stringPlain text representation of the concept
... code SΣ1..1CodeableConcept69548-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
.... id0..1stringUnique id for inter-element referencing
.... extension0..*ExtensionAdditional content defined by implementations
.... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
..... id0..1stringUnique id for inter-element referencing
..... extension0..*ExtensionAdditional content defined by implementations
..... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
..... version0..1stringVersion of the system - if relevant
..... code1..1codeSymbol in syntax defined by the system
Fixed Value: 69548-6
..... display0..1stringRepresentation defined by the system
..... userSelected0..1booleanIf this coding was chosen directly by the user
.... text0..1stringPlain text representation of the concept
... subject SΣ0..1Reference(Cancer Patient Profile)Who and/or what the observation is about
... focus ΣTU0..*Reference(Resource)What the observation is about, when it is not about the subject of record
... encounter Σ0..1Reference(Encounter)Healthcare event during which this observation is made
... Slices for effective[x] SΣ0..1Clinically relevant time/time-period for observation
Slice: Unordered, Open by type:$this
.... effectiveDateTimedateTime
.... effectivePeriodPeriod
.... effectiveTimingTiming
.... effectiveInstantinstant
.... effective[x]:effectiveDateTime SΣ0..1dateTimeClinically relevant time/time-period for observation
... issued Σ0..1instantDate/Time this version was made available
... performer Σ0..*Reference(Practitioner | PractitionerRole | Organization | CareTeam | Patient | RelatedPerson)Who is responsible for the observation
... Slices for value[x] SΣC0..1CodeableConceptActual result
Slice: Unordered, Closed by type:$this
.... value[x]:valueCodeableConcept ΣC0..1CodeableConceptIndeterminate | No call | Present | Absent.
Binding: LOINC Answer List LL1971-2 (required)
... dataAbsentReason SC0..1CodeableConceptWhy the result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


... note 0..*CodedAnnotationComments about the Observation that also contain a coded type
... bodySite 0..1CodeableConceptObserved body part
Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality.

... method S0..1CodeableConceptSequencing | SNP array | PCR | Computational analysis | ...
Binding: LOINC Answer List LL4048-6 (extensible)
... specimen S0..1Reference(Human Specimen Profile)Specimen used for this observation
... device 0..1Reference(Device | DeviceMetric)(Measurement) Device
... referenceRange C0..*BackboneElementNot used in this profile
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... low C0..1SimpleQuantityLow Range, if relevant
.... high C0..1SimpleQuantityHigh Range, if relevant
.... type 0..1CodeableConceptReference range qualifier
Binding: ObservationReferenceRangeMeaningCodes (preferred): Code for the meaning of a reference range.

.... appliesTo 0..*CodeableConceptReference range population
Binding: ObservationReferenceRangeAppliesToCodes (example): Codes identifying the population the reference range applies to.


.... age 0..1RangeApplicable age range, if relevant
.... text 0..1stringText based reference range in an observation
... hasMember Σ0..*Reference(Observation | QuestionnaireResponse | MolecularSequence)Not used in this profile
... derivedFrom Σ0..*Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence)Related measurements the observation is made from
... Slices for component SΣ0..*BackboneElementComponent results
Slice: Unordered, Open by pattern:code
.... component:All Slices Content/Rules for all slices
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example): Codes identifying names of simple observations.

..... value[x] Σ0..1Actual component result
...... valueQuantityQuantity
...... valueCodeableConceptCodeableConcept
...... valueStringstring
...... valueBooleanboolean
...... valueIntegerinteger
...... valueRangeRange
...... valueRatioRatio
...... valueSampledDataSampledData
...... valueTimetime
...... valueDateTimedateTime
...... valuePeriodPeriod
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:conclusion-string Σ0..1BackboneElementClinical Conclusion
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptconclusion-string
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: conclusion-string
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ0..1stringSummary conclusion (interpretation/impression)
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:gene-studied SΣ0..*BackboneElementGene Studied
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code SΣ1..1CodeableConcept48018-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48018-6
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] SΣ1..1CodeableConceptThe HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used.
Binding: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible)
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:cytogenetic-location SΣ0..*BackboneElementCytogenetic (Chromosome) Location
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code SΣ1..1CodeableConcept48001-2
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48001-2
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] SΣ1..1CodeableConceptExample: 1q21.1
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:reference-sequence-assembly Σ0..*BackboneElementHuman Reference Sequence Assembly
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConcept62374-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 62374-4
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1CodeableConceptGRCh37 | GRCh38 | ...
Binding: LOINC Answer List LL1040-6 (extensible)
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:coding-hgvs Σ0..1BackboneElementCoding (cDNA) Change - cHGVS
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConcept48004-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48004-6
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1CodeableConceptA valid HGVS-formatted 'c.' string, e.g. NM_005228.5:c.2369C>T.
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:genomic-hgvs SΣ0..1BackboneElementGenomic (gDNA) Change - gHGVS
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code SΣ1..1CodeableConcept81290-9
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81290-9
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] SΣ1..1CodeableConceptA valid HGVS-formatted 'g.' string, e.g. NC_000016.9:g.2124200_2138612dup
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:cytogenomic-nomenclature SΣ0..1BackboneElementCytogenomic Nomenclature (ISCN)
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code SΣ1..1CodeableConcept81291-7
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81291-7
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] SΣ1..1CodeableConceptActual component result
Binding: (unbound) (example): Binding not yet defined

..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:genomic-ref-seq Σ0..1BackboneElementGenomic Reference Sequence
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConcept48013-7
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48013-7
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1CodeableConceptVersioned genomic reference sequence identifier
Binding: (unbound) (example): Multiple bindings acceptable (NCBI or LRG)

..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:transcript-ref-seq Σ0..1BackboneElementReference Transcript
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConcept51958-7
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 51958-7
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1CodeableConceptVersioned transcript reference sequence identifier
Binding: (unbound) (example): Multiple bindings acceptable (NCBI or LRG)

..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:exact-start-end Σ0..1BackboneElementExact Start-End
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConcept81254-5
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81254-5
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ0..1RangeRange in question. 'High' can be omitted for single nucleotide variants.
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:inner-start-end Σ0..1BackboneElementInner Start-End
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConcept81302-2
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81302-2
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ0..1RangeImprecise variant inner-bounding range
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:outer-start-end Σ0..1BackboneElementOuter Start-End
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConcept81301-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81301-4
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ0..1RangeImprecise variant outer-bounding range
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:coordinate-system Σ0..1BackboneElementCoordinate System
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConcept92822-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 92822-6
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1CodeableConcept0-based interval counting | 0-based character counting | 1-based character counting
Binding: LOINC Answer List LL5323-2 (extensible)
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:ref-allele Σ0..1BackboneElementGenomic Ref Allele
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConcept69547-8
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 69547-8
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ0..1stringNormalized string per the VCF format.
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:alt-allele Σ0..1BackboneElementGenomic Alt Allele
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConcept69551-0
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 69551-0
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ0..1stringNormalized string per the VCF format.
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:coding-change-type SΣ0..1BackboneElementCoding DNA Change Type
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code SΣ1..1CodeableConcept48019-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48019-4
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] SΣ1..1CodeableConceptdeletion | insertion | delins | SNV | copy_number_gain | copy_number_loss | ... (many)
Binding: DNA Change Type (extensible): Concepts in sequence ontology under SO:0002072

..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:genomic-source-class SΣ0..1BackboneElementGenomic Source Class
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code SΣ1..1CodeableConcept48002-0
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48002-0
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] SΣ1..1CodeableConceptGermline | Somatic | Fetal | Likely germline | Likely somatic | Likely fetal | Unknown genomic origin | De novo
Binding: LOINC Answer List LL378-1 (extensible)
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:sample-allelic-frequency SΣ0..1BackboneElementSample Allelic Frequency
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code SΣ1..1CodeableConcept81258-6
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81258-6
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] SΣ0..1QuantityRelative frequency in the sample
...... id 0..1stringUnique id for inter-element referencing
...... extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
...... value Σ0..1decimalNumerical value (with implicit precision)
...... comparator ?!Σ0..1code< | <= | >= | > - how to understand the value
Binding: QuantityComparator (required): How the Quantity should be understood and represented.

...... unit Σ0..1stringUnit representation
...... system ΣC0..1uriSystem that defines coded unit form
Required Pattern: http://unitsofmeasure.org
...... code Σ0..1codeCoded form of the unit
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:allelic-read-depth Σ0..1BackboneElementAllelic Read Depth
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConcept82121-5
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 82121-5
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ0..1QuantityUnfiltered count of supporting reads
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:allelic-state SΣ0..1BackboneElementAllelic State
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code SΣ1..1CodeableConcept53034-5
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 53034-5
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] SΣ1..1CodeableConceptHeteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous
Binding: LOINC Answer List LL381-5 (extensible)
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:variant-inheritance Σ0..1BackboneElementVariant Inheritance
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptvariant-inheritance
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: variant-inheritance
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1CodeableConceptMaternal | Paternal | Unknown
Binding: Variant Inheritances (extensible)
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:variation-code SΣ0..*BackboneElementVariation Code
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code SΣ1..1CodeableConcept81252-9
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81252-9
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] SΣ1..1CodeableConceptClinVar ID or similar
Binding: (unbound) (example): Multiple bindings acceptable

..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:chromosome-identifier Σ0..*BackboneElementChromosome Identifier
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConcept48000-4
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48000-4
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1CodeableConceptChromosome 1 | Chromosome 2 | ... | Chromosome 22 | Chromosome X | Chromosome Y
Binding: LOINC Answer List LL2938-0 (required)
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:protein-hgvs SΣ0..1BackboneElementProtein (Amino Acid) Change - pHGVS
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code SΣ1..1CodeableConcept48005-3
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48005-3
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] SΣ1..1CodeableConceptA valid HGVS-formatted 'p.' string, e.g. NP_000050.2:p.(Asn1836Lys)
Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:amino-acid-change-type SΣ0..1BackboneElementAmino Acid Change Type
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code SΣ1..1CodeableConcept48006-1
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48006-1
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] SΣ1..1CodeableConceptWild type | Deletion | Duplication | Frameshift | Initiating Methionine | Insertion | Insertion and Deletion | Missense | Nonsense | Silent
Binding: LOINC Answer List LL380-7 (extensible)
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:molecular-consequence SΣ0..1BackboneElementMolecular Consequence
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code SΣ1..1CodeableConceptmolecular-consequence
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: molecular-consequence
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] SΣ1..1CodeableConceptstop_lost | stop_gained | inframe_insertion | frameshift_variant | ... (many)
Binding: Molecular Consequence (extensible): Concepts in sequence ontology under SO:0001537.

..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:copy-number SΣ0..1BackboneElementGenomic Structural Variant Copy Number
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code SΣ1..1CodeableConcept82155-3
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 82155-3
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] SΣC0..1QuantityActual component result
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result
.... component:variant-confidence-status Σ0..1BackboneElementVariant Confidence Status
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code Σ1..1CodeableConceptvariant-confidence-status
Binding: LOINCCodes (example): Codes identifying names of simple observations.


Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: variant-confidence-status
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] Σ1..1CodeableConceptHigh | Intermediate | Low
Binding: Variant Confidence Status (required)
..... dataAbsentReason C0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.

..... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.


..... referenceRange 0..*See referenceRange (Observation)Provides guide for interpretation of component result

doco Documentation for this format

Terminology Bindings

PathConformanceValueSet / Code
Observation.languagepreferredCommonLanguages
Additional Bindings Purpose
AllLanguages Max Binding
Observation.statusrequiredObservationStatus
Observation.categorypreferredObservationCategoryCodes
Observation.category:labCategorypreferredPattern: laboratory
Observation.codeexamplePattern: LOINC code 69548-6
Observation.value[x]:valueCodeableConceptrequiredLOINC LL1971-2
Observation.dataAbsentReasonextensibleDataAbsentReason
Observation.interpretationextensibleObservationInterpretationCodes
Observation.bodySiteexampleSNOMEDCTBodyStructures
Observation.methodextensibleLOINC LL4048-6
Observation.referenceRange.typepreferredObservationReferenceRangeMeaningCodes
Observation.referenceRange.appliesToexampleObservationReferenceRangeAppliesToCodes
Observation.component.codeexampleLOINCCodes (a valid code from LOINC)
Observation.component.dataAbsentReasonextensibleDataAbsentReason
Observation.component.interpretationextensibleObservationInterpretationCodes
Observation.component:conclusion-string.codeexamplePattern: conclusion-string
Observation.component:conclusion-string.dataAbsentReasonextensibleDataAbsentReason
Observation.component:conclusion-string.interpretationextensibleObservationInterpretationCodes
Observation.component:gene-studied.codeexamplePattern: LOINC code 48018-6
Observation.component:gene-studied.value[x]extensibleHGNCVS
Observation.component:gene-studied.dataAbsentReasonextensibleDataAbsentReason
Observation.component:gene-studied.interpretationextensibleObservationInterpretationCodes
Observation.component:cytogenetic-location.codeexamplePattern: LOINC code 48001-2
Observation.component:cytogenetic-location.dataAbsentReasonextensibleDataAbsentReason
Observation.component:cytogenetic-location.interpretationextensibleObservationInterpretationCodes
Observation.component:reference-sequence-assembly.codeexamplePattern: LOINC code 62374-4
Observation.component:reference-sequence-assembly.value[x]extensibleLOINC LL1040-6
Observation.component:reference-sequence-assembly.dataAbsentReasonextensibleDataAbsentReason
Observation.component:reference-sequence-assembly.interpretationextensibleObservationInterpretationCodes
Observation.component:coding-hgvs.codeexamplePattern: LOINC code 48004-6
Observation.component:coding-hgvs.value[x]requiredHGVSVS
Observation.component:coding-hgvs.dataAbsentReasonextensibleDataAbsentReason
Observation.component:coding-hgvs.interpretationextensibleObservationInterpretationCodes
Observation.component:genomic-hgvs.codeexamplePattern: LOINC code 81290-9
Observation.component:genomic-hgvs.value[x]requiredHGVSVS
Observation.component:genomic-hgvs.dataAbsentReasonextensibleDataAbsentReason
Observation.component:genomic-hgvs.interpretationextensibleObservationInterpretationCodes
Observation.component:cytogenomic-nomenclature.codeexamplePattern: LOINC code 81291-7
Observation.component:cytogenomic-nomenclature.value[x]example
Observation.component:cytogenomic-nomenclature.dataAbsentReasonextensibleDataAbsentReason
Observation.component:cytogenomic-nomenclature.interpretationextensibleObservationInterpretationCodes
Observation.component:genomic-ref-seq.codeexamplePattern: LOINC code 48013-7
Observation.component:genomic-ref-seq.value[x]example
Observation.component:genomic-ref-seq.dataAbsentReasonextensibleDataAbsentReason
Observation.component:genomic-ref-seq.interpretationextensibleObservationInterpretationCodes
Observation.component:transcript-ref-seq.codeexamplePattern: LOINC code 51958-7
Observation.component:transcript-ref-seq.value[x]example
Observation.component:transcript-ref-seq.dataAbsentReasonextensibleDataAbsentReason
Observation.component:transcript-ref-seq.interpretationextensibleObservationInterpretationCodes
Observation.component:exact-start-end.codeexamplePattern: LOINC code 81254-5
Observation.component:exact-start-end.dataAbsentReasonextensibleDataAbsentReason
Observation.component:exact-start-end.interpretationextensibleObservationInterpretationCodes
Observation.component:inner-start-end.codeexamplePattern: LOINC code 81302-2
Observation.component:inner-start-end.dataAbsentReasonextensibleDataAbsentReason
Observation.component:inner-start-end.interpretationextensibleObservationInterpretationCodes
Observation.component:outer-start-end.codeexamplePattern: LOINC code 81301-4
Observation.component:outer-start-end.dataAbsentReasonextensibleDataAbsentReason
Observation.component:outer-start-end.interpretationextensibleObservationInterpretationCodes
Observation.component:coordinate-system.codeexamplePattern: LOINC code 92822-6
Observation.component:coordinate-system.value[x]extensibleLOINC LL5323-2
Observation.component:coordinate-system.dataAbsentReasonextensibleDataAbsentReason
Observation.component:coordinate-system.interpretationextensibleObservationInterpretationCodes
Observation.component:ref-allele.codeexamplePattern: LOINC code 69547-8
Observation.component:ref-allele.dataAbsentReasonextensibleDataAbsentReason
Observation.component:ref-allele.interpretationextensibleObservationInterpretationCodes
Observation.component:alt-allele.codeexamplePattern: LOINC code 69551-0
Observation.component:alt-allele.dataAbsentReasonextensibleDataAbsentReason
Observation.component:alt-allele.interpretationextensibleObservationInterpretationCodes
Observation.component:coding-change-type.codeexamplePattern: LOINC code 48019-4
Observation.component:coding-change-type.value[x]extensibleDNAChangeTypeVS
Observation.component:coding-change-type.dataAbsentReasonextensibleDataAbsentReason
Observation.component:coding-change-type.interpretationextensibleObservationInterpretationCodes
Observation.component:genomic-source-class.codeexamplePattern: LOINC code 48002-0
Observation.component:genomic-source-class.value[x]extensibleLOINC LL378-1
Observation.component:genomic-source-class.dataAbsentReasonextensibleDataAbsentReason
Observation.component:genomic-source-class.interpretationextensibleObservationInterpretationCodes
Observation.component:sample-allelic-frequency.codeexamplePattern: LOINC code 81258-6
Observation.component:sample-allelic-frequency.value[x].comparatorrequiredQuantityComparator
Observation.component:sample-allelic-frequency.dataAbsentReasonextensibleDataAbsentReason
Observation.component:sample-allelic-frequency.interpretationextensibleObservationInterpretationCodes
Observation.component:allelic-read-depth.codeexamplePattern: LOINC code 82121-5
Observation.component:allelic-read-depth.dataAbsentReasonextensibleDataAbsentReason
Observation.component:allelic-read-depth.interpretationextensibleObservationInterpretationCodes
Observation.component:allelic-state.codeexamplePattern: LOINC code 53034-5
Observation.component:allelic-state.value[x]extensibleLOINC LL381-5
Observation.component:allelic-state.dataAbsentReasonextensibleDataAbsentReason
Observation.component:allelic-state.interpretationextensibleObservationInterpretationCodes
Observation.component:variant-inheritance.codeexamplePattern: variant-inheritance
Observation.component:variant-inheritance.value[x]extensibleVariantInheritanceVS
Observation.component:variant-inheritance.dataAbsentReasonextensibleDataAbsentReason
Observation.component:variant-inheritance.interpretationextensibleObservationInterpretationCodes
Observation.component:variation-code.codeexamplePattern: LOINC code 81252-9
Observation.component:variation-code.value[x]example
Observation.component:variation-code.dataAbsentReasonextensibleDataAbsentReason
Observation.component:variation-code.interpretationextensibleObservationInterpretationCodes
Observation.component:chromosome-identifier.codeexamplePattern: LOINC code 48000-4
Observation.component:chromosome-identifier.value[x]requiredLOINC LL2938-0
Observation.component:chromosome-identifier.dataAbsentReasonextensibleDataAbsentReason
Observation.component:chromosome-identifier.interpretationextensibleObservationInterpretationCodes
Observation.component:protein-hgvs.codeexamplePattern: LOINC code 48005-3
Observation.component:protein-hgvs.value[x]requiredHGVSVS
Observation.component:protein-hgvs.dataAbsentReasonextensibleDataAbsentReason
Observation.component:protein-hgvs.interpretationextensibleObservationInterpretationCodes
Observation.component:amino-acid-change-type.codeexamplePattern: LOINC code 48006-1
Observation.component:amino-acid-change-type.value[x]extensibleLOINC LL380-7
Observation.component:amino-acid-change-type.dataAbsentReasonextensibleDataAbsentReason
Observation.component:amino-acid-change-type.interpretationextensibleObservationInterpretationCodes
Observation.component:molecular-consequence.codeexamplePattern: molecular-consequence
Observation.component:molecular-consequence.value[x]extensibleMolecularConsequenceVS
Observation.component:molecular-consequence.dataAbsentReasonextensibleDataAbsentReason
Observation.component:molecular-consequence.interpretationextensibleObservationInterpretationCodes
Observation.component:copy-number.codeexamplePattern: LOINC code 82155-3
Observation.component:copy-number.dataAbsentReasonextensibleDataAbsentReason
Observation.component:copy-number.interpretationextensibleObservationInterpretationCodes
Observation.component:variant-confidence-status.codeexamplePattern: variant-confidence-status
Observation.component:variant-confidence-status.value[x]requiredVariantConfidenceStatusVS
Observation.component:variant-confidence-status.dataAbsentReasonextensibleDataAbsentReason
Observation.component:variant-confidence-status.interpretationextensibleObservationInterpretationCodes

This structure is derived from Variant

Summary

Must-Support: 50 elements

Structures

This structure refers to these other structures:

Slices

This structure defines the following Slices:

  • The element Observation.effective[x] is sliced based on the value of type:$this

Maturity: 1

 

Other representations of profile: CSV, Excel, Schematron