R4 Draft for Comment

This page is part of the FHIR Specification (v3.2.0: R4 Ballot 1). The current version which supercedes this version is 5.0.0. For a full list of available versions, see the Directory of published versions . Page versions: R4B R4

Extension: Variant

Orders and Observations Work Group Maturity Level: 1InformativeUse Context: Any

URL for this extension: 

http://hl7.org/fhir/StructureDefinition/observation-geneticsVariant

Status: draft. Extension maintained by: Health Level Seven International (Clinical Genomics)

Variant information.

Context of Use: Use on element: Observation

usage info: insert a list of places where this extension is used

Extension Content

Summary

NameFlagsCard.TypeDescription & Constraintsdoco
.. extension0..1ExtensionURL = http://hl7.org/fhir/StructureDefinition/observation-geneticsVariant
Variant: Variant information.
Use on element: Observation
... Name0..1CodeableConceptHuman Genome Variation Society (HGVS) nomenclature for a single or set of DNA Sequence Variation(s) identified in testing. The use of the nomenclature is also used to describe non-variations (aka. wild types). LOINC Code: ([48004-6](http://loinc.org/48004-6)).
... Id0..1CodeableConceptIdentifier for DNA sequence variant. If a germline variant, ClinVar or dbSNP identifier should be used. If a somatic variant, COSMIC identifier should be used, unless in ClinVar then either maybe used. Need to provide the code system used (ClinVar, dbSNP, COSMIC) LOINC Code: ([48003-8](http://loinc.org/48003-8)).
... Type0..1CodeableConceptCodified type for associated DNA sequence variant. DNA sequence variants use the HGVS notation, which implies the DNA sequence variant type. LOINC Code: ([48019-4](http://loinc.org/48019-4)).

doco Documentation for this format

Full Structure

NameFlagsCard.TypeDescription & Constraintsdoco
.. extension0..1ExtensionURL = http://hl7.org/fhir/StructureDefinition/observation-geneticsVariant
Variant: Variant information.
Use on element: Observation
... extension 0..1ExtensionHGVS nomenclature for observed DNA sequence variant
.... url 1..1uri"Name"
.... valueCodeableConcept 0..1CodeableConceptValue of extension
Binding: ???? (preferred)
... extension 0..1ExtensionDNA sequence variant ID
.... url 1..1uri"Id"
.... valueCodeableConcept 0..1CodeableConceptValue of extension
... extension 0..1ExtensionDNA sequence variant type
.... url 1..1uri"Type"
.... valueCodeableConcept 0..1CodeableConceptValue of extension
... url 1..1uri"http://hl7.org/fhir/StructureDefinition/observation-geneticsVariant"
... value[x] 0..0

doco Documentation for this format

XML Template

<!-- Variant -->doco

<extension xmlns="http://hl7.org/fhir"
     url="http://hl7.org/fhir/StructureDefinition/observation-geneticsVariant" >
 <-- extension sliced by value:url  in the specified orderOpen-->
 <extension url="Name"> 0..1 Extension  <!-- 0..1 HGVS nomenclature for observed DNA sequence variant -->
  <valueCodeableConcept><!-- 0..1 CodeableConcept Value of extension --></valueCodeableConcept>
 </extension>
 <extension url="Id"> 0..1 Extension  <!-- 0..1 DNA sequence variant ID -->
  <valueCodeableConcept><!-- 0..1 CodeableConcept 
      Value of extension --></valueCodeableConcept>
 </extension>
 <extension url="Type"> 0..1 Extension  <!-- 0..1 DNA sequence variant type -->
  <valueCodeableConcept><!-- 0..1 CodeableConcept 
      Value of extension --></valueCodeableConcept>
 </extension>
</extension>

JSON Template

{ // Variant
    "extension" : [ //  sliced by value:url  in the specified order, Open 
      { // HGVS nomenclature for observed DNA sequence variant //
        // from Element: extension
        "extension" : [ //  sliced by value:url  in the specified order, Open ]
        "url" : "Name", // R! 
        "valueCodeableConcept" : { CodeableConcept } //Value of extension
      },
      { // DNA sequence variant ID //
        // from Element: extension
        "extension" : [ //  sliced by value:url  in the specified order, Open ]
        "url" : "Id", // R! 
        "valueCodeableConcept" : { CodeableConcept } //Value of extension
      },
      { // DNA sequence variant type //
        // from Element: extension
        "extension" : [ //  sliced by value:url  in the specified order, Open ]
        "url" : "Type", // R! 
        "valueCodeableConcept" : { CodeableConcept } //Value of extension
      }
    ],
    "url" : "http://hl7.org/fhir/StructureDefinition/observation-geneticsVariant", // R! 
// value[x]: Value of extension. One of these 46:
  }

Summary

NameFlagsCard.TypeDescription & Constraintsdoco
.. extension0..1ExtensionURL = http://hl7.org/fhir/StructureDefinition/observation-geneticsVariant
Variant: Variant information.
Use on element: Observation
... Name0..1CodeableConceptHuman Genome Variation Society (HGVS) nomenclature for a single or set of DNA Sequence Variation(s) identified in testing. The use of the nomenclature is also used to describe non-variations (aka. wild types). LOINC Code: ([48004-6](http://loinc.org/48004-6)).
... Id0..1CodeableConceptIdentifier for DNA sequence variant. If a germline variant, ClinVar or dbSNP identifier should be used. If a somatic variant, COSMIC identifier should be used, unless in ClinVar then either maybe used. Need to provide the code system used (ClinVar, dbSNP, COSMIC) LOINC Code: ([48003-8](http://loinc.org/48003-8)).
... Type0..1CodeableConceptCodified type for associated DNA sequence variant. DNA sequence variants use the HGVS notation, which implies the DNA sequence variant type. LOINC Code: ([48019-4](http://loinc.org/48019-4)).

doco Documentation for this format

Full Structure

NameFlagsCard.TypeDescription & Constraintsdoco
.. extension0..1ExtensionURL = http://hl7.org/fhir/StructureDefinition/observation-geneticsVariant
Variant: Variant information.
Use on element: Observation
... extension 0..1ExtensionHGVS nomenclature for observed DNA sequence variant
.... url 1..1uri"Name"
.... valueCodeableConcept 0..1CodeableConceptValue of extension
Binding: ???? (preferred)
... extension 0..1ExtensionDNA sequence variant ID
.... url 1..1uri"Id"
.... valueCodeableConcept 0..1CodeableConceptValue of extension
... extension 0..1ExtensionDNA sequence variant type
.... url 1..1uri"Type"
.... valueCodeableConcept 0..1CodeableConceptValue of extension
... url 1..1uri"http://hl7.org/fhir/StructureDefinition/observation-geneticsVariant"
... value[x] 0..0

doco Documentation for this format

XML Template

<!-- Variant -->doco

<extension xmlns="http://hl7.org/fhir"
     url="http://hl7.org/fhir/StructureDefinition/observation-geneticsVariant" >
 <-- extension sliced by value:url  in the specified orderOpen-->
 <extension url="Name"> 0..1 Extension  <!-- 0..1 HGVS nomenclature for observed DNA sequence variant -->
  <valueCodeableConcept><!-- 0..1 CodeableConcept Value of extension --></valueCodeableConcept>
 </extension>
 <extension url="Id"> 0..1 Extension  <!-- 0..1 DNA sequence variant ID -->
  <valueCodeableConcept><!-- 0..1 CodeableConcept 
      Value of extension --></valueCodeableConcept>
 </extension>
 <extension url="Type"> 0..1 Extension  <!-- 0..1 DNA sequence variant type -->
  <valueCodeableConcept><!-- 0..1 CodeableConcept 
      Value of extension --></valueCodeableConcept>
 </extension>
</extension>

JSON Template

{ // Variant
    "extension" : [ //  sliced by value:url  in the specified order, Open 
      { // HGVS nomenclature for observed DNA sequence variant //
        // from Element: extension
        "extension" : [ //  sliced by value:url  in the specified order, Open ]
        "url" : "Name", // R! 
        "valueCodeableConcept" : { CodeableConcept } //Value of extension
      },
      { // DNA sequence variant ID //
        // from Element: extension
        "extension" : [ //  sliced by value:url  in the specified order, Open ]
        "url" : "Id", // R! 
        "valueCodeableConcept" : { CodeableConcept } //Value of extension
      },
      { // DNA sequence variant type //
        // from Element: extension
        "extension" : [ //  sliced by value:url  in the specified order, Open ]
        "url" : "Type", // R! 
        "valueCodeableConcept" : { CodeableConcept } //Value of extension
      }
    ],
    "url" : "http://hl7.org/fhir/StructureDefinition/observation-geneticsVariant", // R! 
// value[x]: Value of extension. One of these 46:
  }

 

Constraints

  • ele-1: All FHIR elements must have a @value or children (xpath: @value|f:*|h:div)
  • ext-1: Must have either extensions or value[x], not both (xpath: exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')]))