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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 ID 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 ID 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).

... 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).

... 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).


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 ID Observation
... extension 0..1ExtensionHGVS nomenclature for observed DNA sequence variant
.... url 1..1uri"Name"
.... valueCodeableConcept 0..1CodeableConceptValue of extension
Binding: ClinVar (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 48:
  }

Summary

NameFlagsCard.TypeDescription & Constraintsdoco
.. extension0..1ExtensionURL = http://hl7.org/fhir/StructureDefinition/observation-geneticsVariant
Variant: Variant information.


Use on Element ID 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).

... 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).

... 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).


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 ID Observation
... extension 0..1ExtensionHGVS nomenclature for observed DNA sequence variant
.... url 1..1uri"Name"
.... valueCodeableConcept 0..1CodeableConceptValue of extension
Binding: ClinVar (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 48:
  }

 

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')]))