R4 Ballot #1 #2 (Mixed Normative/Trial use)

This page is part of the FHIR Specification (v3.3.0: (v3.5.0: R4 Ballot 2). #2). 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 : 1 Informative Use 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 ID Observation

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

Extension Content

Summary

Name Flags Card. Type Description & Constraints doco
. . extension Variant 0..1 Extension URL = http://hl7.org/fhir/StructureDefinition/observation-geneticsVariant
Variant: Variant information.


Use on Element ID Observation
. . . Name 0..1 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 0..1 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 0..1 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 ).


doco Documentation for this format

Full Structure

Name Flags Card. Type Description & Constraints doco
. . extension 0..1 Extension URL = http://hl7.org/fhir/StructureDefinition/observation-geneticsVariant
Variant: Variant information.


Use on Element ID Observation
. . . extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
. . . extension 0..1 Extension HGVS nomenclature for observed DNA sequence variant
. . . . extension 0..0
. . . . url 1..1 uri "Name"
. . . . valueCodeableConcept 0..1 CodeableConcept Value of extension
Binding: ClinVar Clin var ( preferred )
. . . extension 0..1 Extension DNA sequence variant ID
. . . . extension 0..0
. . . . url 1..1 uri "Id"
. . . . valueCodeableConcept 0..1 CodeableConcept Value of extension
. . . extension 0..1 Extension DNA sequence variant type
. . . . extension 0..0
. . . . url 1..1 uri "Type"
. . . . valueCodeableConcept 0..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

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>

  <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 49:
  }

Summary

Name Flags Card. Type Description & Constraints doco
. . extension Variant 0..1 Extension URL = http://hl7.org/fhir/StructureDefinition/observation-geneticsVariant
Variant: Variant information.


Use on Element ID Observation
. . . Name 0..1 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 0..1 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 0..1 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 ).


doco Documentation for this format

Full Structure

Name Flags Card. Type Description & Constraints doco
. . extension 0..1 Extension URL = http://hl7.org/fhir/StructureDefinition/observation-geneticsVariant
Variant: Variant information.


Use on Element ID Observation
. . . extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
. . . extension 0..1 Extension HGVS nomenclature for observed DNA sequence variant
. . . . extension 0..0
. . . . url 1..1 uri "Name"
. . . . valueCodeableConcept 0..1 CodeableConcept Value of extension
Binding: ClinVar Clin var ( preferred )
. . . extension 0..1 Extension DNA sequence variant ID
. . . . extension 0..0
. . . . url 1..1 uri "Id"
. . . . valueCodeableConcept 0..1 CodeableConcept Value of extension
. . . extension 0..1 Extension DNA sequence variant type
. . . . extension 0..0
. . . . url 1..1 uri "Type"
. . . . valueCodeableConcept 0..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

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>

  <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 49:
  }

 

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')]) )