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Extension: Variant

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

Extension Content

• Summary
• Full Structure
• XML
• JSON
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Summary

Name	Flags	Card.	Type	Description & Constraints
Variant		0..1	Extension	URL = http://hl7.org/fhir/StructureDefinition/observation-geneticsVariant Variant: Variant information. Use on Element ID Observation
Name		0..1	CodeableConcept	The material on this page will be removed in a future release. This content is deprecated and SHOULD NOT be used. Implementers are instead directed to the (Genomics Reporting Implementation Guide) for guidance. 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).
Documentation for this format

Full Structure

Name	Flags	Card.	Type	Description & Constraints
extension		0..1	Extension	URL = http://hl7.org/fhir/StructureDefinition/observation-geneticsVariant Variant: Variant information. Use on Element ID Observation
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: ClinVar (preferred): NCBI central repository for curating pathogenicity 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"
value[x]		0..0
valueBase64Binary			base64Binary
valueBoolean			boolean
valueCanonical			canonical(Any)
valueCode			code
valueDate			date
valueDateTime			dateTime
valueDecimal			decimal
valueId			id
valueInstant			instant
valueInteger			integer
valueMarkdown			markdown
valueOid			oid
valuePositiveInt			positiveInt
valueString			string
valueTime			time
valueUnsignedInt			unsignedInt
valueUri			uri
valueUrl			url
valueUuid			uuid
valueAddress			Address
valueAge			Age
valueAnnotation			Annotation
valueAttachment			Attachment
valueCodeableConcept			CodeableConcept
valueCodeableReference			CodeableReference
valueCoding			Coding
valueContactPoint			ContactPoint
valueCount			Count
valueDistance			Distance
valueDuration			Duration
valueHumanName			HumanName
valueIdentifier			Identifier
valueMoney			Money
valuePeriod			Period
valueQuantity			Quantity
valueRange			Range
valueRatio			Ratio
valueRatioRange			RatioRange
valueReference			Reference(Any)
valueSampledData			SampledData
valueSignature			Signature
valueTiming			Timing
valueContactDetail			ContactDetail
valueContributor			Contributor
valueDataRequirement			DataRequirement
valueExpression			Expression
valueParameterDefinition			ParameterDefinition
valueRelatedArtifact			RelatedArtifact
valueTriggerDefinition			TriggerDefinition
valueUsageContext			UsageContext
valueDosage			Dosage
Documentation for this format

XML Template

<!-- Variant -->

<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><!--  1..1 CodeableConcept Value of extension --></valueCodeableConcept>
 </extension>
 <extension url="Id">  0..1 Extension  <!--  0..1 DNA sequence variant ID -->
  <valueCodeableConcept><!--  1..1 CodeableConcept 
      Value of extension --></valueCodeableConcept>
 </extension>
 <extension url="Type">  0..1 Extension  <!--  0..1 DNA sequence variant type -->
  <valueCodeableConcept><!--  1..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 // C?
        // from Element: extension
        "extension" : [ //  sliced by value:url  in the specified order, Open ]
        "url" : "Name", // R! 
        "valueCodeableConcept" : { CodeableConcept } // C? R! Value of extension
      },
      { // DNA sequence variant ID // C?
        // from Element: extension
        "extension" : [ //  sliced by value:url  in the specified order, Open ]
        "url" : "Id", // R! 
        "valueCodeableConcept" : { CodeableConcept } // C? R! Value of extension
      },
      { // DNA sequence variant type // C?
        // from Element: extension
        "extension" : [ //  sliced by value:url  in the specified order, Open ]
        "url" : "Type", // R! 
        "valueCodeableConcept" : { CodeableConcept } // C? R! Value of extension
      }
    ],
    "url" : "http://hl7.org/fhir/StructureDefinition/observation-geneticsVariant", // R! 
// value[x]: Value of extension. One of these 51:
  }

Summary

Name	Flags	Card.	Type	Description & Constraints
Variant		0..1	Extension	URL = http://hl7.org/fhir/StructureDefinition/observation-geneticsVariant Variant: Variant information. Use on Element ID Observation
Name		0..1	CodeableConcept	The material on this page will be removed in a future release. This content is deprecated and SHOULD NOT be used. Implementers are instead directed to the (Genomics Reporting Implementation Guide) for guidance. 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).
Documentation for this format

Full Structure

Name	Flags	Card.	Type	Description & Constraints
extension		0..1	Extension	URL = http://hl7.org/fhir/StructureDefinition/observation-geneticsVariant Variant: Variant information. Use on Element ID Observation
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: ClinVar (preferred): NCBI central repository for curating pathogenicity 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"
value[x]		0..0
valueBase64Binary			base64Binary
valueBoolean			boolean
valueCanonical			canonical(Any)
valueCode			code
valueDate			date
valueDateTime			dateTime
valueDecimal			decimal
valueId			id
valueInstant			instant
valueInteger			integer
valueMarkdown			markdown
valueOid			oid
valuePositiveInt			positiveInt
valueString			string
valueTime			time
valueUnsignedInt			unsignedInt
valueUri			uri
valueUrl			url
valueUuid			uuid
valueAddress			Address
valueAge			Age
valueAnnotation			Annotation
valueAttachment			Attachment
valueCodeableConcept			CodeableConcept
valueCodeableReference			CodeableReference
valueCoding			Coding
valueContactPoint			ContactPoint
valueCount			Count
valueDistance			Distance
valueDuration			Duration
valueHumanName			HumanName
valueIdentifier			Identifier
valueMoney			Money
valuePeriod			Period
valueQuantity			Quantity
valueRange			Range
valueRatio			Ratio
valueRatioRange			RatioRange
valueReference			Reference(Any)
valueSampledData			SampledData
valueSignature			Signature
valueTiming			Timing
valueContactDetail			ContactDetail
valueContributor			Contributor
valueDataRequirement			DataRequirement
valueExpression			Expression
valueParameterDefinition			ParameterDefinition
valueRelatedArtifact			RelatedArtifact
valueTriggerDefinition			TriggerDefinition
valueUsageContext			UsageContext
valueDosage			Dosage
Documentation for this format

XML Template

<!-- Variant -->

<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><!--  1..1 CodeableConcept Value of extension --></valueCodeableConcept>
 </extension>
 <extension url="Id">  0..1 Extension  <!--  0..1 DNA sequence variant ID -->
  <valueCodeableConcept><!--  1..1 CodeableConcept 
      Value of extension --></valueCodeableConcept>
 </extension>
 <extension url="Type">  0..1 Extension  <!--  0..1 DNA sequence variant type -->
  <valueCodeableConcept><!--  1..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 // C?
        // from Element: extension
        "extension" : [ //  sliced by value:url  in the specified order, Open ]
        "url" : "Name", // R! 
        "valueCodeableConcept" : { CodeableConcept } // C? R! Value of extension
      },
      { // DNA sequence variant ID // C?
        // from Element: extension
        "extension" : [ //  sliced by value:url  in the specified order, Open ]
        "url" : "Id", // R! 
        "valueCodeableConcept" : { CodeableConcept } // C? R! Value of extension
      },
      { // DNA sequence variant type // C?
        // from Element: extension
        "extension" : [ //  sliced by value:url  in the specified order, Open ]
        "url" : "Type", // R! 
        "valueCodeableConcept" : { CodeableConcept } // C? R! Value of extension
      }
    ],
    "url" : "http://hl7.org/fhir/StructureDefinition/observation-geneticsVariant", // R! 
// value[x]: Value of extension. One of these 51:
  }

Constraints

• ele-1: All FHIR elements must have a @value or children unless an empty Parameters resource (xpath: @value|f:*|h:div|self::f:Parameters)
• ext-1: Must have either extensions or value[x], not both (xpath: exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')]))
• ele-1: On Extension.extension: All FHIR elements must have a @value or children (xpath on Extension.extension: @value|f:*|h:div)
• ext-1: On Extension.extension: Must have either extensions or value[x], not both (xpath on Extension.extension: exists(f:extension)!=exists(f:*[starts-with(local-name(.), "value")]))
• ele-1: On Extension.extension: All FHIR elements must have a @value or children (xpath on Extension.extension: @value|f:*|h:div)
• ext-1: On Extension.extension: Must have either extensions or value[x], not both (xpath on Extension.extension: exists(f:extension)!=exists(f:*[starts-with(local-name(.), "value")]))
• ele-1: On Extension.extension.extension: All FHIR elements must have a @value or children (xpath on Extension.extension.extension: @value|f:*|h:div)
• ext-1: On Extension.extension.extension: Must have either extensions or value[x], not both (xpath on Extension.extension.extension: exists(f:extension)!=exists(f:*[starts-with(local-name(.), "value")]))
• ele-1: On Extension.extension.value[x]: All FHIR elements must have a @value or children (xpath on Extension.extension.value[x]: @value|f:*|h:div)
• ele-1: On Extension.extension: All FHIR elements must have a @value or children (xpath on Extension.extension: @value|f:*|h:div)
• ext-1: On Extension.extension: Must have either extensions or value[x], not both (xpath on Extension.extension: exists(f:extension)!=exists(f:*[starts-with(local-name(.), "value")]))
• ele-1: On Extension.extension.extension: All FHIR elements must have a @value or children (xpath on Extension.extension.extension: @value|f:*|h:div)
• ext-1: On Extension.extension.extension: Must have either extensions or value[x], not both (xpath on Extension.extension.extension: exists(f:extension)!=exists(f:*[starts-with(local-name(.), "value")]))
• ele-1: On Extension.extension.value[x]: All FHIR elements must have a @value or children (xpath on Extension.extension.value[x]: @value|f:*|h:div)
• ele-1: On Extension.extension: All FHIR elements must have a @value or children (xpath on Extension.extension: @value|f:*|h:div)
• ext-1: On Extension.extension: Must have either extensions or value[x], not both (xpath on Extension.extension: exists(f:extension)!=exists(f:*[starts-with(local-name(.), "value")]))
• ele-1: On Extension.extension.extension: All FHIR elements must have a @value or children (xpath on Extension.extension.extension: @value|f:*|h:div)
• ext-1: On Extension.extension.extension: Must have either extensions or value[x], not both (xpath on Extension.extension.extension: exists(f:extension)!=exists(f:*[starts-with(local-name(.), "value")]))
• ele-1: On Extension.extension.value[x]: All FHIR elements must have a @value or children (xpath on Extension.extension.value[x]: @value|f:*|h:div)
• ele-1: On Extension.value[x]: All FHIR elements must have a @value or children (xpath on Extension.value[x]: @value|f:*|h:div)