description: Observation-related profiles
package_name: hl7.fhir.uv.genomics
derivation: constraint
name: Variant
type: Observation
elements:
  code:
    short: Genetic variant assessment
    type: CodeableConcept
    mustSupport: false
    pattern:
      type: CodeableConcept
      value:
        coding:
        - {code: 69548-6, system: 'http://loinc.org'}
    index: 0
  value:
    short: Present|Absent|No call|Indeterminate
    mustSupport: false
    choices: [valueCodeableConcept]
    index: 2
  valueCodeableConcept: {short: Present|Absent|No call|Indeterminate, type: CodeableConcept, mustSupport: false, choiceOf: value, index: 3}
  method:
    short: Sequencing | Oligo aCGH | SNP array | BAC aCGH |Curated|+
    binding: {strength: extensible, valueSet: 'http://loinc.org/vs/LL4048-6'}
    mustSupport: false
    index: 4
  component:
    mustSupport: false
    index: 5
    slicing:
      rules: open
      discriminator:
      - {path: code, type: pattern}
      min: null
      slices:
        alt-allele:
          match:
            code:
              coding:
              - {code: 69551-0, system: 'http://loinc.org'}
          schema:
            short: Genomic alt allele
            mustSupport: false
            index: 88
            elements:
              code:
                type: CodeableConcept
                mustSupport: false
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 69551-0, system: 'http://loinc.org'}
                index: 89
              value:
                mustSupport: false
                choices: [valueString]
                index: 91
              valueString: {type: string, mustSupport: false, choiceOf: value, index: 92}
            required: [valueString, value, code]
        functional-annotation:
          match:
            code:
              coding:
              - {code: functional-annotation, system: 'http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes'}
          schema:
            short: Functional Annotation
            mustSupport: false
            array: true
            index: 16
            elements:
              code:
                type: CodeableConcept
                mustSupport: false
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: functional-annotation, system: 'http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes'}
                index: 17
              value:
                short: Concepts in sequence ontology under SO:0001537 (see http://www.sequenceontology.org/browser/current_release/term/SO:0001537)
                mustSupport: false
                choices: [valueCodeableConcept]
                index: 19
              valueCodeableConcept: {short: 'Concepts in sequence ontology under SO:0001537 (see http://www.sequenceontology.org/browser/current_release/term/SO:0001537)', type: CodeableConcept, mustSupport: false, choiceOf: value, index: 20}
            required: [value, valueCodeableConcept, code]
        allelic-state:
          match:
            code:
              coding:
              - {code: 53034-5, system: 'http://loinc.org'}
          schema:
            short: Allelic state
            mustSupport: false
            index: 73
            elements:
              code:
                type: CodeableConcept
                mustSupport: false
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 53034-5, system: 'http://loinc.org'}
                index: 74
              value:
                short: Heteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous
                mustSupport: false
                choices: [valueCodeableConcept]
                index: 76
              valueCodeableConcept: {short: Heteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous, type: CodeableConcept, mustSupport: false, choiceOf: value, index: 77}
            required: [value, valueCodeableConcept, code]
        allelic-read-depth:
          match:
            code:
              coding:
              - {code: 82121-5, system: 'http://loinc.org'}
          schema:
            short: Allelic read depth
            mustSupport: false
            array: true
            index: 68
            elements:
              code:
                type: CodeableConcept
                mustSupport: false
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 82121-5, system: 'http://loinc.org'}
                index: 69
              value:
                mustSupport: false
                choices: [valueQuantity]
                index: 71
              valueQuantity: {type: Quantity, mustSupport: false, choiceOf: value, index: 72}
            required: [value, valueQuantity, code]
        outer-start-end:
          match:
            code:
              coding:
              - {code: outer-start-end, system: 'http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes'}
          schema:
            short: Variant outer start and end
            mustSupport: false
            index: 110
            elements:
              code:
                type: CodeableConcept
                mustSupport: false
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: outer-start-end, system: 'http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes'}
                index: 111
              value:
                mustSupport: false
                choices: [valueRange]
                index: 113
              valueRange: {type: Range, mustSupport: false, choiceOf: value, index: 114}
              value[x]:
                elements:
                  low: {mustSupport: false, index: 115}
                  high: {mustSupport: false, index: 116}
                required: [low, high]
            required: [valueRange, value, code]
        genomic-source-class:
          match:
            code:
              coding:
              - {code: 48002-0, system: 'http://loinc.org'}
          schema:
            short: Genomic source class
            mustSupport: false
            index: 36
            elements:
              code:
                type: CodeableConcept
                mustSupport: false
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 48002-0, system: 'http://loinc.org'}
                index: 37
              value:
                short: Germline | Somatic | Fetal | Likely germline | Likely somatic |Likely fetal | Unknown genomic origin | De novo
                mustSupport: false
                choices: [valueCodeableConcept]
                index: 39
              valueCodeableConcept: {short: Germline | Somatic | Fetal | Likely germline | Likely somatic |Likely fetal | Unknown genomic origin | De novo, type: CodeableConcept, mustSupport: false, choiceOf: value, index: 40}
            required: [value, valueCodeableConcept, code]
        copy-number:
          match:
            code:
              coding:
              - {code: 82155-3, system: 'http://loinc.org'}
          schema:
            short: Genomic structural variant copy number
            mustSupport: false
            index: 78
            elements:
              code:
                type: CodeableConcept
                mustSupport: false
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 82155-3, system: 'http://loinc.org'}
                index: 79
              value:
                mustSupport: false
                choices: [valueQuantity]
                index: 81
              valueQuantity: {type: Quantity, mustSupport: false, choiceOf: value, index: 82}
            required: [value, valueQuantity, code]
        variant-length:
          match:
            code:
              coding:
              - {code: 81300-6, system: 'http://loinc.org'}
          schema:
            short: Structural variant length
            mustSupport: false
            index: 105
            elements:
              code:
                type: CodeableConcept
                mustSupport: false
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 81300-6, system: 'http://loinc.org'}
                index: 106
              value:
                mustSupport: false
                choices: [valueQuantity]
                index: 108
              valueQuantity: {type: Quantity, mustSupport: false, choiceOf: value, index: 109}
            required: [value, valueQuantity, code]
        arrCGH-ratio:
          match:
            code:
              coding:
              - {code: 81299-0, system: 'http://loinc.org'}
          schema:
            short: Structural variant reported arrCGH [Ratio]
            mustSupport: false
            index: 129
            elements:
              code:
                type: CodeableConcept
                mustSupport: false
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 81299-0, system: 'http://loinc.org'}
                index: 130
              value:
                mustSupport: false
                choices: [valueQuantity]
                index: 132
              valueQuantity: {type: Quantity, mustSupport: false, choiceOf: value, index: 133}
            required: [value, valueQuantity, code]
        amino-acid-chg-type:
          match:
            code:
              coding:
              - {code: 48006-1, system: 'http://loinc.org'}
          schema:
            short: Amino acid change type
            mustSupport: false
            index: 46
            elements:
              code:
                type: CodeableConcept
                mustSupport: false
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 48006-1, system: 'http://loinc.org'}
                index: 47
              value:
                short: Wild type | Deletion | Duplication | Frameshift | Initiating Methionine | Insertion | Insertion and Deletion | Missense | Silent | Stop Codon Mutation
                mustSupport: false
                choices: [valueCodeableConcept]
                index: 49
              valueCodeableConcept: {short: Wild type | Deletion | Duplication | Frameshift | Initiating Methionine | Insertion | Insertion and Deletion | Missense | Silent | Stop Codon Mutation, type: CodeableConcept, mustSupport: false, choiceOf: value, index: 50}
            required: [value, valueCodeableConcept, code]
        variation-code:
          match:
            code:
              coding:
              - {code: 81252-9, system: 'http://loinc.org'}
          schema:
            short: Variation Code
            mustSupport: false
            index: 21
            elements:
              code:
                type: CodeableConcept
                mustSupport: false
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 81252-9, system: 'http://loinc.org'}
                index: 22
              value:
                mustSupport: false
                choices: [valueCodeableConcept]
                index: 24
              valueCodeableConcept: {type: CodeableConcept, mustSupport: false, choiceOf: value, index: 25}
            required: [value, valueCodeableConcept, code]
        exact-start-end:
          match:
            code:
              coding:
              - {code: exact-start-end, system: 'http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes'}
          schema:
            short: Exact start-end
            mustSupport: false
            index: 98
            elements:
              code:
                type: CodeableConcept
                mustSupport: false
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: exact-start-end, system: 'http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes'}
                index: 99
              value:
                mustSupport: false
                choices: [valueRange]
                index: 101
              valueRange: {type: Range, mustSupport: false, choiceOf: value, index: 102}
              value[x]:
                elements:
                  low: {short: Exact Start, mustSupport: false, index: 103}
                  high: {short: Exact End, mustSupport: false, index: 104}
                required: [low]
            required: [valueRange, value, code]
        ref-allele:
          match:
            code:
              coding:
              - {code: 69547-8, system: 'http://loinc.org'}
          schema:
            short: Genomic ref allele
            mustSupport: false
            index: 83
            elements:
              code:
                type: CodeableConcept
                mustSupport: false
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 69547-8, system: 'http://loinc.org'}
                index: 84
              value:
                mustSupport: false
                choices: [valueString]
                index: 86
              valueString: {type: string, mustSupport: false, choiceOf: value, index: 87}
            required: [valueString, value, code]
        genomic-dna-chg:
          match:
            code:
              coding:
              - {code: 81290-9, system: 'http://loinc.org'}
          schema:
            short: DNA Change - Genomic (gHGVS)
            mustSupport: false
            index: 31
            elements:
              code:
                type: CodeableConcept
                mustSupport: false
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 81290-9, system: 'http://loinc.org'}
                index: 32
              value:
                mustSupport: false
                choices: [valueCodeableConcept]
                index: 34
              valueCodeableConcept: {type: CodeableConcept, mustSupport: false, choiceOf: value, index: 35}
            required: [value, valueCodeableConcept, code]
        amino-acid-chg:
          match:
            code:
              coding:
              - {code: 48005-3, system: 'http://loinc.org'}
          schema:
            short: Amino acid change (pHGVS)
            mustSupport: false
            index: 41
            elements:
              code:
                type: CodeableConcept
                mustSupport: false
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 48005-3, system: 'http://loinc.org'}
                index: 42
              value:
                mustSupport: false
                choices: [valueCodeableConcept]
                index: 44
              valueCodeableConcept: {type: CodeableConcept, mustSupport: false, choiceOf: value, index: 45}
            required: [value, valueCodeableConcept, code]
        inner-start-end:
          match:
            code:
              coding:
              - {code: inner-start-end, system: 'http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes'}
          schema:
            short: Variant inner start and end
            mustSupport: false
            index: 117
            elements:
              code:
                type: CodeableConcept
                mustSupport: false
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: inner-start-end, system: 'http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes'}
                index: 118
              value:
                mustSupport: false
                choices: [valueRange]
                index: 120
              valueRange: {type: Range, mustSupport: false, choiceOf: value, index: 121}
              value[x]:
                elements:
                  low: {mustSupport: false, index: 122}
                  high: {mustSupport: false, index: 123}
                required: [low, high]
            required: [valueRange, value, code]
        transcript-ref-seq:
          match:
            code:
              coding:
              - {code: 51958-7, system: 'http://loinc.org'}
          schema:
            short: Transcript reference sequence ID
            mustSupport: false
            index: 51
            elements:
              code:
                type: CodeableConcept
                mustSupport: false
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 51958-7, system: 'http://loinc.org'}
                index: 52
              value:
                mustSupport: false
                choices: [valueCodeableConcept]
                index: 54
              valueCodeableConcept: {type: CodeableConcept, mustSupport: false, choiceOf: value, index: 55}
            required: [value, valueCodeableConcept, code]
        dna-chg:
          match:
            code:
              coding:
              - {code: 48004-6, system: 'http://loinc.org'}
          schema:
            short: DNA Change - Transcript (cHGVS)
            mustSupport: false
            index: 6
            elements:
              code:
                type: CodeableConcept
                mustSupport: false
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 48004-6, system: 'http://loinc.org'}
                index: 7
              value:
                mustSupport: false
                choices: [valueCodeableConcept]
                index: 9
              valueCodeableConcept: {type: CodeableConcept, mustSupport: false, choiceOf: value, index: 10}
            required: [value, valueCodeableConcept, code]
        sample-allelic-frequency:
          match:
            code:
              coding:
              - {code: 81258-6, system: 'http://loinc.org'}
          schema:
            short: Sample Allelic Frequency
            mustSupport: false
            index: 61
            elements:
              code:
                short: Sample Sample VAF
                type: CodeableConcept
                mustSupport: false
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 81258-6, system: 'http://loinc.org'}
                index: 62
              value:
                mustSupport: false
                choices: [valueQuantity]
                index: 64
              valueQuantity: {type: Quantity, mustSupport: false, choiceOf: value, index: 65}
              value[x]:
                elements:
                  value: {mustSupport: false, index: 66}
                  system:
                    type: uri
                    pattern: {type: Uri, value: 'http://unitsofmeasure.org'}
                    mustSupport: false
                    index: 67
                required: [value, system]
            required: [value, valueQuantity, code]
        genomic-ref-seq:
          match:
            code:
              coding:
              - {code: 48013-7, system: 'http://loinc.org'}
          schema:
            short: Genomic reference sequence ID
            mustSupport: false
            index: 56
            elements:
              code:
                type: CodeableConcept
                mustSupport: false
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 48013-7, system: 'http://loinc.org'}
                index: 57
              value:
                mustSupport: false
                choices: [valueCodeableConcept]
                index: 59
              valueCodeableConcept: {type: CodeableConcept, mustSupport: false, choiceOf: value, index: 60}
            required: [value, valueCodeableConcept, code]
        cytogenomic-nomenclature:
          match:
            code:
              coding:
              - {code: 81291-7, system: 'http://loinc.org'}
          schema:
            short: Cytogenomic Nomenclature
            mustSupport: false
            index: 139
            elements:
              code:
                short: Variant ISCN
                type: CodeableConcept
                mustSupport: false
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 81291-7, system: 'http://loinc.org'}
                index: 140
              value:
                mustSupport: false
                choices: [valueCodeableConcept]
                index: 142
              valueCodeableConcept: {type: CodeableConcept, mustSupport: false, choiceOf: value, index: 143}
            required: [value, valueCodeableConcept, code]
        variant-inheritance:
          match:
            code:
              coding:
              - {code: variant-inheritance, system: 'http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes'}
          schema:
            short: Variant Inheritance
            mustSupport: false
            index: 144
            elements:
              code:
                type: CodeableConcept
                mustSupport: false
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: variant-inheritance, system: 'http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes'}
                index: 145
              value:
                mustSupport: false
                choices: [valueCodeableConcept]
                index: 147
              valueCodeableConcept: {type: CodeableConcept, mustSupport: false, choiceOf: value, index: 148}
            required: [value, valueCodeableConcept, code]
        dna-chg-type:
          match:
            code:
              coding:
              - {code: 48019-4, system: 'http://loinc.org'}
          schema:
            short: DNA change type
            mustSupport: false
            index: 11
            elements:
              code:
                type: CodeableConcept
                mustSupport: false
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 48019-4, system: 'http://loinc.org'}
                index: 12
              value:
                short: Concepts in sequence ontology under SO:0002072 (see http://www.sequenceontology.org/browser/current_release/term/SO:0002072)
                mustSupport: false
                choices: [valueCodeableConcept]
                index: 14
              valueCodeableConcept: {short: 'Concepts in sequence ontology under SO:0002072 (see http://www.sequenceontology.org/browser/current_release/term/SO:0002072)', type: CodeableConcept, mustSupport: false, choiceOf: value, index: 15}
            required: [value, valueCodeableConcept, code]
        chromosome-copy-number-change-type:
          match:
            code:
              coding:
              - {code: 62378-5, system: 'http://loinc.org'}
          schema:
            short: Chromosome copy number change type
            mustSupport: false
            index: 124
            elements:
              code:
                type: CodeableConcept
                mustSupport: false
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 62378-5, system: 'http://loinc.org'}
                index: 125
              value:
                short: Copy number gain | Copy number loss
                mustSupport: false
                choices: [valueCodeableConcept]
                index: 127
              valueCodeableConcept: {short: Copy number gain | Copy number loss, type: CodeableConcept, mustSupport: false, choiceOf: value, index: 128}
            required: [value, valueCodeableConcept, code]
        dbSNP-id:
          match:
            code:
              coding:
              - {code: 81255-2, system: 'http://loinc.org'}
          schema:
            short: dbSNP ID
            mustSupport: false
            index: 26
            elements:
              code:
                type: CodeableConcept
                mustSupport: false
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 81255-2, system: 'http://loinc.org'}
                index: 27
              value:
                mustSupport: false
                choices: [valueCodeableConcept]
                index: 29
              valueCodeableConcept: {type: CodeableConcept, mustSupport: false, choiceOf: value, index: 30}
            required: [value, valueCodeableConcept, code]
        coordinate-system:
          match:
            code:
              coding:
              - {code: 92822-6, system: 'http://loinc.org'}
          schema:
            short: Coordinate System
            mustSupport: false
            index: 93
            elements:
              code:
                type: CodeableConcept
                mustSupport: false
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 92822-6, system: 'http://loinc.org'}
                index: 94
              value:
                short: 0-based interval | 0-based character | 1-based character
                mustSupport: false
                choices: [valueCodeableConcept]
                index: 96
              valueCodeableConcept: {type: CodeableConcept, short: 0-based interval | 0-based character | 1-based character, mustSupport: false, choiceOf: value, index: 97}
            required: [value, valueCodeableConcept, code]
        complex-var-type:
          match:
            code:
              coding:
              - {code: 81263-6, system: 'http://loinc.org'}
          schema:
            short: Complex variant type
            mustSupport: false
            index: 134
            elements:
              code:
                type: CodeableConcept
                mustSupport: false
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 81263-6, system: 'http://loinc.org'}
                index: 135
              value:
                short: Compound heterozygous | Double heterozygous | Haplotype | Hemizygous
                mustSupport: false
                choices: [valueCodeableConcept]
                index: 137
              valueCodeableConcept: {short: Compound heterozygous | Double heterozygous | Haplotype | Hemizygous, type: CodeableConcept, mustSupport: false, choiceOf: value, index: 138}
            required: [value, valueCodeableConcept, code]
package_version: reporting-1.0.0
class: profile
kind: resource
url: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant
base: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/finding
version: 1.0.0
required: [value, valueCodeableConcept, code]