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. For a full list of available versions, see the Directory of published versions

Extension: Allele

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

Allele 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This extension has been replaced by the profiles and extensions defined in the Genomics Reporting Guide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: Allele information.

    • Name: CodeableConcept: An allele is one of a set of coexisting sequence variants of a gene (SO:0001023). This element is the common name for the allele. LOINC Code: (48008-7).
    • State: CodeableConcept: The level of occurrence of a single DNA Sequence Variant within a set of chromosomes. Heterozygous indicates the DNA sequence variant is only present in one of the two genes contained in homologous chromosomes. Homozygous indicates the DNA Sequence Variant is present in both genes contained in homologous chromosomes. Hemizygous indicates the DNA Sequence Variant exists in the only single copy of a gene in a non-homologous chromosome (the male X and Y chromosome are non-homologous). Hemiplasmic indicates that the DNA Sequence Variant is present in some but not all of the copies of mitochondrial DNA. Homoplasmic indicates that the DNA Sequence Variant is present in all of the copies of mitochondrial DNA. LOINC Code: (53034-5).
    • Frequency: decimal: A physical quality which inheres to the allele by virtue of the number instances of the allele within a population. LOINC Code: (81258-6).

    Maturity: 1

    This structure is derived from Extension

    NameFlagsCard.TypeDescription & Constraintsdoco
    .. Extension 0..1 Extension Allele
    ... Slices for extension Content/Rules for all slices
    .... extension:Name 0..1 Extension Name of allele
    ..... extension 0..0
    ..... url 1..1 uri "Name"
    ..... value[x] 1..1 CodeableConcept Value of extension
    Binding Description (No ValueSet): (example): EMBL-EBI database of AlleleName.

    .... extension:State 0..1 Extension The level of occurrence of a single DNA sequence variant within a set of chromosomes: Heteroplasmic / Homoplasmic / Homozygous / Heterozygous / Hemizygous
    ..... extension 0..0
    ..... url 1..1 uri "State"
    ..... value[x] 1..1 CodeableConcept Value of extension
    .... extension:Frequency 0..1 Extension Allele frequency
    ..... extension 0..0
    ..... url 1..1 uri "Frequency"
    ..... value[x] 1..1 decimal Value of extension
    ... url 1..1 uri "http://hl7.org/fhir/StructureDefinition/observation-geneticsAllele"
    ... value[x] 0..0

    doco Documentation for this format
    NameFlagsCard.TypeDescription & Constraintsdoco
    .. Extension 0..1 Extension Allele
    ... 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 Name of allele
    ..... 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): EMBL-EBI database of AlleleName.

    .... extension:State 0..1 Extension The level of occurrence of a single DNA sequence variant within a set of chromosomes: Heteroplasmic / Homoplasmic / Homozygous / Heterozygous / Hemizygous
    ..... id 0..1 id Unique id for inter-element referencing
    ..... extension 0..0
    ..... url 1..1 uri "State"
    ..... value[x] 1..1 CodeableConcept Value of extension
    .... extension:Frequency 0..1 Extension Allele frequency
    ..... id 0..1 id Unique id for inter-element referencing
    ..... extension 0..0
    ..... url 1..1 uri "Frequency"
    ..... value[x] 1..1 decimal Value of extension
    ... url 1..1 uri "http://hl7.org/fhir/StructureDefinition/observation-geneticsAllele"

    doco Documentation for this format

    This structure is derived from Extension

    Summary

    Complex Extension: Allele information.

    • Name: CodeableConcept: An allele is one of a set of coexisting sequence variants of a gene (SO:0001023). This element is the common name for the allele. LOINC Code: (48008-7).
    • State: CodeableConcept: The level of occurrence of a single DNA Sequence Variant within a set of chromosomes. Heterozygous indicates the DNA sequence variant is only present in one of the two genes contained in homologous chromosomes. Homozygous indicates the DNA Sequence Variant is present in both genes contained in homologous chromosomes. Hemizygous indicates the DNA Sequence Variant exists in the only single copy of a gene in a non-homologous chromosome (the male X and Y chromosome are non-homologous). Hemiplasmic indicates that the DNA Sequence Variant is present in some but not all of the copies of mitochondrial DNA. Homoplasmic indicates that the DNA Sequence Variant is present in all of the copies of mitochondrial DNA. LOINC Code: (53034-5).
    • Frequency: decimal: A physical quality which inheres to the allele by virtue of the number instances of the allele within a population. LOINC Code: (81258-6).

    Maturity: 1

    Differential View

    This structure is derived from Extension

    NameFlagsCard.TypeDescription & Constraintsdoco
    .. Extension 0..1 Extension Allele
    ... Slices for extension Content/Rules for all slices
    .... extension:Name 0..1 Extension Name of allele
    ..... extension 0..0
    ..... url 1..1 uri "Name"
    ..... value[x] 1..1 CodeableConcept Value of extension
    Binding Description (No ValueSet): (example): EMBL-EBI database of AlleleName.

    .... extension:State 0..1 Extension The level of occurrence of a single DNA sequence variant within a set of chromosomes: Heteroplasmic / Homoplasmic / Homozygous / Heterozygous / Hemizygous
    ..... extension 0..0
    ..... url 1..1 uri "State"
    ..... value[x] 1..1 CodeableConcept Value of extension
    .... extension:Frequency 0..1 Extension Allele frequency
    ..... extension 0..0
    ..... url 1..1 uri "Frequency"
    ..... value[x] 1..1 decimal Value of extension
    ... url 1..1 uri "http://hl7.org/fhir/StructureDefinition/observation-geneticsAllele"
    ... value[x] 0..0

    doco Documentation for this format

    Snapshot View

    NameFlagsCard.TypeDescription & Constraintsdoco
    .. Extension 0..1 Extension Allele
    ... 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 Name of allele
    ..... 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): EMBL-EBI database of AlleleName.

    .... extension:State 0..1 Extension The level of occurrence of a single DNA sequence variant within a set of chromosomes: Heteroplasmic / Homoplasmic / Homozygous / Heterozygous / Hemizygous
    ..... id 0..1 id Unique id for inter-element referencing
    ..... extension 0..0
    ..... url 1..1 uri "State"
    ..... value[x] 1..1 CodeableConcept Value of extension
    .... extension:Frequency 0..1 Extension Allele frequency
    ..... id 0..1 id Unique id for inter-element referencing
    ..... extension 0..0
    ..... url 1..1 uri "Frequency"
    ..... value[x] 1..1 decimal Value of extension
    ... url 1..1 uri "http://hl7.org/fhir/StructureDefinition/observation-geneticsAllele"

    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)