FHIR Extensions Pack
5.2.0-ballot - 5.2.0 Ballot - September 2024) International flag

FHIR Extensions Pack, published by HL7 International / FHIR Infrastructure. This guide is not an authorized publication; it is the continuous build for version 5.2.0-ballot built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/fhir-extensions/ and changes regularly. See the Directory of published versions

Extension: Variant

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

Variant information.

Context of Use

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)