FHIR Extensions Pack
5.2.0 - February 2025 International flag

This page is part of the FHIR Core Extensions Registry (v5.2.0: Release 5.2) based on FHIR (HL7® FHIR® Standard) v5.0.0. This is the current published version in its permanent home (it will always be available at this URL). For a full list of available versions, see the Directory of published versions

Extension: Variant

Official URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsVariant Version: 5.2.0
Standards status: Deprecated Maturity Level: 1 Responsible: HL7 International / Orders and Observations Computable Name: Variant

Variant information.

Context of Use

This extension is deprecated and should no longer be used

This extension has been replaced by the profiles and extensions defined in the Genomics Reporting Guide

This extension may be used on the following element(s):

Usage info

Usage:

  • This Extension is not used by any profiles in this Implementation Guide

Changes since version 1.0.0:

  • New Content

    • Formal Views of Extension Content

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

    This structure is derived from Extension

    Summary

    Complex Extension: Variant information.

    • Name: CodeableConcept: Human 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).
    • Id: CodeableConcept: Identifier 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).
    • Type: CodeableConcept: Codified type for associated DNA sequence variant. DNA sequence variants use the HGVS notation, which implies the DNA sequence variant type. LOINC Code: (48019-4).

    Maturity: 1

    This structure is derived from Extension

    NameFlagsCard.TypeDescription & Constraintsdoco
    .. Extension 0..1 Extension Variant
    ... Slices for extension Content/Rules for all slices
    .... extension:Name 0..1 Extension HGVS nomenclature for observed DNA sequence variant
    ..... extension 0..0
    ..... url 1..1 uri "Name"
    ..... value[x] 1..1 CodeableConcept Value of extension
    Binding Description (No ValueSet): (example): NCBI central repository of potentially clinically relevant variants.

    .... extension:Id 0..1 Extension DNA sequence variant ID
    ..... extension 0..0
    ..... url 1..1 uri "Id"
    ..... value[x] 1..1 CodeableConcept Value of extension
    .... extension:Type 0..1 Extension DNA sequence variant type
    ..... extension 0..0
    ..... url 1..1 uri "Type"
    ..... value[x] 1..1 CodeableConcept Value of extension
    ... url 1..1 uri "http://hl7.org/fhir/StructureDefinition/observation-geneticsVariant"
    ... value[x] 0..0

    doco Documentation for this format
    NameFlagsCard.TypeDescription & Constraintsdoco
    .. Extension 0..1 Extension Variant
    ... id 0..1 id Unique id for inter-element referencing
    ... Slices for extension 0..* Extension Additional content defined by implementations
    Slice: Unordered, Open by value:url
    .... extension:Name 0..1 Extension HGVS nomenclature for observed DNA sequence variant
    ..... id 0..1 id Unique id for inter-element referencing
    ..... extension 0..0
    ..... url 1..1 uri "Name"
    ..... value[x] 1..1 CodeableConcept Value of extension
    Binding Description (No ValueSet): (example): NCBI central repository of potentially clinically relevant variants.

    .... extension:Id 0..1 Extension DNA sequence variant ID
    ..... id 0..1 id Unique id for inter-element referencing
    ..... extension 0..0
    ..... url 1..1 uri "Id"
    ..... value[x] 1..1 CodeableConcept Value of extension
    .... extension:Type 0..1 Extension DNA sequence variant type
    ..... id 0..1 id Unique id for inter-element referencing
    ..... extension 0..0
    ..... url 1..1 uri "Type"
    ..... value[x] 1..1 CodeableConcept Value of extension
    ... url 1..1 uri "http://hl7.org/fhir/StructureDefinition/observation-geneticsVariant"

    doco Documentation for this format

    This structure is derived from Extension

    Summary

    Complex Extension: Variant information.

    • Name: CodeableConcept: Human 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).
    • Id: CodeableConcept: Identifier 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).
    • Type: CodeableConcept: Codified type for associated DNA sequence variant. DNA sequence variants use the HGVS notation, which implies the DNA sequence variant type. LOINC Code: (48019-4).

    Maturity: 1

    Differential View

    This structure is derived from Extension

    NameFlagsCard.TypeDescription & Constraintsdoco
    .. Extension 0..1 Extension Variant
    ... Slices for extension Content/Rules for all slices
    .... extension:Name 0..1 Extension HGVS nomenclature for observed DNA sequence variant
    ..... extension 0..0
    ..... url 1..1 uri "Name"
    ..... value[x] 1..1 CodeableConcept Value of extension
    Binding Description (No ValueSet): (example): NCBI central repository of potentially clinically relevant variants.

    .... extension:Id 0..1 Extension DNA sequence variant ID
    ..... extension 0..0
    ..... url 1..1 uri "Id"
    ..... value[x] 1..1 CodeableConcept Value of extension
    .... extension:Type 0..1 Extension DNA sequence variant type
    ..... extension 0..0
    ..... url 1..1 uri "Type"
    ..... value[x] 1..1 CodeableConcept Value of extension
    ... url 1..1 uri "http://hl7.org/fhir/StructureDefinition/observation-geneticsVariant"
    ... value[x] 0..0

    doco Documentation for this format

    Snapshot View

    NameFlagsCard.TypeDescription & Constraintsdoco
    .. Extension 0..1 Extension Variant
    ... id 0..1 id Unique id for inter-element referencing
    ... Slices for extension 0..* Extension Additional content defined by implementations
    Slice: Unordered, Open by value:url
    .... extension:Name 0..1 Extension HGVS nomenclature for observed DNA sequence variant
    ..... id 0..1 id Unique id for inter-element referencing
    ..... extension 0..0
    ..... url 1..1 uri "Name"
    ..... value[x] 1..1 CodeableConcept Value of extension
    Binding Description (No ValueSet): (example): NCBI central repository of potentially clinically relevant variants.

    .... extension:Id 0..1 Extension DNA sequence variant ID
    ..... id 0..1 id Unique id for inter-element referencing
    ..... extension 0..0
    ..... url 1..1 uri "Id"
    ..... value[x] 1..1 CodeableConcept Value of extension
    .... extension:Type 0..1 Extension DNA sequence variant type
    ..... id 0..1 id Unique id for inter-element referencing
    ..... extension 0..0
    ..... url 1..1 uri "Type"
    ..... value[x] 1..1 CodeableConcept Value of extension
    ... url 1..1 uri "http://hl7.org/fhir/StructureDefinition/observation-geneticsVariant"

    doco Documentation for this format

     

    Other representations of profile: CSV, Excel, Schematron

    Terminology Bindings

    PathConformanceValueSetURI
    Extension.extension:Name.value[x]example

    Constraints

    IdGradePath(s)DetailsRequirements
    ele-1error**ALL** elementsAll FHIR elements must have a @value or children
    : hasValue() or (children().count() > id.count())
    ext-1error**ALL** extensionsMust have either extensions or value[x], not both
    : extension.exists() != value.exists()

    Search Parameters for this Extension

    (none found)