description: Details about a set of changes in the tested sample compared to a reference sequence.
package_name: hl7.fhir.uv.genomics-reporting
derivation: constraint
name: Variant
type: Observation
elements:
  code:
    short: 69548-6
    pattern:
      type: CodeableConcept
      value:
        coding:
        - {code: 69548-6, system: 'http://loinc.org'}
    index: 0
  value:
    choices: []
    index: 2
    slicing:
      rules: open
      ordered: false
      discriminator:
      - {path: $this, type: type}
      min: null
      slices:
        valueCodeableConcept:
          match: {}
          schema:
            short: Indeterminate | No call | Present | Absent.
            choices: [valueCodeableConcept]
            index: 4
          min: 0
          max: 1
  valueCodeableConcept:
    short: Indeterminate | No call | Present | Absent.
    type: CodeableConcept
    choiceOf: value
    index: 5
    slicing:
      slices:
        valueCodeableConcept:
          match: {}
          schema: {short: Indeterminate | No call | Present | Absent., type: CodeableConcept, choiceOf: value, index: 5}
          min: 0
          max: 1
  method:
    short: Sequencing | SNP array | PCR | Computational analysis | ...
    binding: {strength: extensible, valueSet: 'http://loinc.org/vs/LL4048-6'}
    index: 6
  component:
    short: DNA change (c.HGVS)
    index: 7
    slicing:
      slices:
        representative-protein-ref-seq:
          match: {}
          schema:
            short: Protein Reference Sequence
            index: 27
            elements:
              code:
                short: protein-ref-seq
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: protein-ref-seq, system: 'http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs'}
                index: 28
              value:
                short: Versioned protein reference sequence identifier
                choices: [valueCodeableConcept]
                index: 30
              valueCodeableConcept: {type: CodeableConcept, short: Versioned protein reference sequence identifier, choiceOf: value, index: 31}
            required: [value, valueCodeableConcept]
        alt-allele:
          match: {}
          schema:
            short: Genomic Alt Allele
            index: 62
            elements:
              code:
                short: 69551-0
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 69551-0, system: 'http://loinc.org'}
                index: 63
              value:
                short: Normalized string per the VCF format.
                choices: [valueString]
                index: 65
              valueString: {type: string, short: Normalized string per the VCF format., choiceOf: value, index: 66}
        variant-inheritance-basis:
          match: {}
          schema:
            short: Evidential basis for variant inheritance
            index: 98
            elements:
              code:
                short: Basis for allelic phase
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 82309-6, system: 'http://loinc.org'}
                index: 99
              value:
                short: Directly measured | Family DNA | Family history | Inferred from population data
                choices: [valueCodeableConcept]
                index: 101
              valueCodeableConcept: {type: CodeableConcept, short: Directly measured | Family DNA | Family history | Inferred from population data, choiceOf: value, index: 102}
            required: [value, valueCodeableConcept]
        allelic-state:
          match: {}
          schema:
            short: Allelic State
            index: 88
            elements:
              code:
                short: 53034-5
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 53034-5, system: 'http://loinc.org'}
                index: 89
              value:
                short: Heteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous
                choices: [valueCodeableConcept]
                index: 91
              valueCodeableConcept: {type: CodeableConcept, short: Heteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous, choiceOf: value, index: 92}
            required: [value, valueCodeableConcept]
        allelic-read-depth:
          match: {}
          schema:
            short: Allelic Read Depth
            index: 83
            elements:
              code:
                short: 82121-5
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 82121-5, system: 'http://loinc.org'}
                index: 84
              value:
                short: Unfiltered count of supporting reads
                choices: [valueQuantity]
                index: 86
              valueQuantity: {type: Quantity, short: Unfiltered count of supporting reads, choiceOf: value, index: 87}
        outer-start-end:
          match: {}
          schema:
            short: Outer Start-End
            index: 47
            elements:
              code:
                short: 81301-4
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 81301-4, system: 'http://loinc.org'}
                index: 48
              value:
                short: Imprecise variant outer-bounding range
                choices: [valueRange]
                index: 50
              valueRange: {type: Range, short: Imprecise variant outer-bounding range, choiceOf: value, index: 51}
        genomic-source-class:
          match: {}
          schema:
            short: Genomic Source Class
            index: 72
            elements:
              code:
                short: 48002-0
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 48002-0, system: 'http://loinc.org'}
                index: 73
              value:
                short: Germline | Somatic | Fetal | Likely germline | Likely somatic | Likely fetal | Unknown genomic origin | De novo
                choices: [valueCodeableConcept]
                index: 75
              valueCodeableConcept: {type: CodeableConcept, short: Germline | Somatic | Fetal | Likely germline | Likely somatic | Likely fetal | Unknown genomic origin | De novo, choiceOf: value, index: 76}
            required: [value, valueCodeableConcept]
        copy-number:
          match: {}
          schema:
            short: Genomic Structural Variant Copy Number
            index: 118
            elements:
              code:
                short: 82155-3
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 82155-3, system: 'http://loinc.org'}
                index: 119
              value:
                choices: [valueQuantity, valueRange]
                index: 121
              valueQuantity: {type: Quantity, choiceOf: value, index: 122}
              valueRange: {type: Range, choiceOf: value, index: 123}
        representative-transcript-ref-seq:
          match: {}
          schema:
            short: Reference Transcript
            index: 32
            elements:
              code:
                short: 51958-7
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 51958-7, system: 'http://loinc.org'}
                index: 33
              value:
                short: Versioned transcript reference sequence identifier
                choices: [valueCodeableConcept]
                index: 35
              valueCodeableConcept: {type: CodeableConcept, short: Versioned transcript reference sequence identifier, choiceOf: value, index: 36}
            required: [value, valueCodeableConcept]
        variation-code:
          match: {}
          schema:
            short: Variation Code
            array: true
            index: 103
            elements:
              code:
                short: 81252-9
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 81252-9, system: 'http://loinc.org'}
                index: 104
              value:
                short: ClinVar ID or similar
                choices: [valueCodeableConcept]
                index: 106
              valueCodeableConcept: {type: CodeableConcept, short: ClinVar ID or similar, choiceOf: value, index: 107}
            required: [value, valueCodeableConcept]
        exact-start-end:
          match: {}
          schema:
            short: Exact Start-End
            index: 37
            elements:
              code:
                short: 81254-5
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 81254-5, system: 'http://loinc.org'}
                index: 38
              value:
                short: Range in question. 'High' can be omitted for single nucleotide variants.
                choices: [valueRange]
                index: 40
              valueRange: {type: Range, short: Range in question. 'High' can be omitted for single nucleotide variants., choiceOf: value, index: 41}
        genomic-hgvs:
          match: {}
          schema:
            short: Genomic (gDNA) Change - gHGVS
            index: 12
            elements:
              code:
                short: 81290-9
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 81290-9, system: 'http://loinc.org'}
                index: 13
              value:
                short: A valid HGVS-formatted 'g.' string, e.g. NC_000016.9:g.2124200_2138612dup
                choices: [valueCodeableConcept]
                index: 15
              valueCodeableConcept: {type: CodeableConcept, short: 'A valid HGVS-formatted ''g.'' string, e.g. NC_000016.9:g.2124200_2138612dup', choiceOf: value, index: 16}
            required: [value, valueCodeableConcept]
        ref-allele:
          match: {}
          schema:
            short: Genomic Ref Allele
            index: 57
            elements:
              code:
                short: 69547-8
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 69547-8, system: 'http://loinc.org'}
                index: 58
              value:
                short: Normalized string per the VCF format.
                choices: [valueString]
                index: 60
              valueString: {type: string, short: Normalized string per the VCF format., choiceOf: value, index: 61}
        inner-start-end:
          match: {}
          schema:
            short: Inner Start-End
            index: 42
            elements:
              code:
                short: 81302-2
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 81302-2, system: 'http://loinc.org'}
                index: 43
              value:
                short: Imprecise variant inner-bounding range
                choices: [valueRange]
                index: 45
              valueRange: {type: Range, short: Imprecise variant inner-bounding range, choiceOf: value, index: 46}
        repeat-number:
          match: {}
          schema:
            short: Repeat Number
            array: true
            index: 135
            extensions:
              repeat-motif-order: {url: 'http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order', min: 0, max: 1, type: Extension, index: 136}
            elements:
              extension:
                type: Extension
                url: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order
                index: 136
                slicing:
                  slices:
                    repeat-motif-order:
                      match: {}
                      schema: {type: Extension, url: 'http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order', index: 136}
                      min: 0
                      max: 1
              code:
                short: repeat-number
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: repeat-number, system: 'http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs'}
                index: 137
              value:
                short: '40'
                choices: [valueQuantity]
                index: 139
              valueQuantity: {type: Quantity, short: '40', choiceOf: value, index: 140}
            required: [value, valueQuantity]
        representative-coding-hgvs:
          match: {}
          schema:
            short: DNA change (c.HGVS)
            index: 7
            elements:
              code:
                short: 48004-6
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 48004-6, system: 'http://loinc.org'}
                index: 8
              value:
                short: A valid HGVS-formatted 'c.' string, e.g. NM_005228.5:c.2369C>T.
                choices: [valueCodeableConcept]
                index: 10
              valueCodeableConcept: {type: CodeableConcept, short: 'A valid HGVS-formatted ''c.'' string, e.g. NM_005228.5:c.2369C>T.', choiceOf: value, index: 11}
            required: [value, valueCodeableConcept]
        variant-confidence-status:
          match: {}
          schema:
            short: Variant Confidence Status
            index: 124
            elements:
              code:
                short: variant-confidence-status
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: variant-confidence-status, system: 'http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs'}
                index: 125
              value:
                short: High | Intermediate | Low
                choices: [valueCodeableConcept]
                index: 127
              valueCodeableConcept: {type: CodeableConcept, short: High | Intermediate | Low, choiceOf: value, index: 128}
            required: [value, valueCodeableConcept]
        sample-allelic-frequency:
          match: {}
          schema:
            short: Sample Allelic Frequency
            index: 77
            elements:
              code:
                short: 81258-6
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 81258-6, system: 'http://loinc.org'}
                index: 78
              value:
                short: Relative frequency in the sample
                choices: [valueQuantity]
                index: 80
              valueQuantity: {type: Quantity, short: Relative frequency in the sample, choiceOf: value, index: 81}
              value[x]:
                elements:
                  system:
                    pattern: {type: Uri, value: 'http://unitsofmeasure.org'}
                    index: 82
        genomic-ref-seq:
          match: {}
          schema:
            short: Genomic Reference Sequence
            index: 22
            elements:
              code:
                short: 48013-7
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 48013-7, system: 'http://loinc.org'}
                index: 23
              value:
                short: Versioned genomic reference sequence identifier
                choices: [valueCodeableConcept]
                index: 25
              valueCodeableConcept: {type: CodeableConcept, short: Versioned genomic reference sequence identifier, choiceOf: value, index: 26}
            required: [value, valueCodeableConcept]
        cytogenomic-nomenclature:
          match: {}
          schema:
            short: Cytogenomic Nomenclature (ISCN)
            index: 17
            elements:
              code:
                short: 81291-7
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 81291-7, system: 'http://loinc.org'}
                index: 18
              value:
                choices: [valueCodeableConcept]
                index: 20
              valueCodeableConcept: {type: CodeableConcept, choiceOf: value, index: 21}
            required: [value, valueCodeableConcept]
        variant-inheritance:
          match: {}
          schema:
            short: Origin of germline genetic variant
            index: 93
            elements:
              code:
                short: 94186-4
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 94186-4, system: 'http://loinc.org'}
                index: 94
              value:
                short: Maternal | Paternal | Unknown
                choices: [valueCodeableConcept]
                index: 96
              valueCodeableConcept: {type: CodeableConcept, short: Maternal | Paternal | Unknown, choiceOf: value, index: 97}
            required: [value, valueCodeableConcept]
        chromosome-identifier:
          match: {}
          schema:
            short: Chromosome Identifier
            array: true
            index: 108
            elements:
              code:
                short: 48000-4
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 48000-4, system: 'http://loinc.org'}
                index: 109
              value:
                short: Chromosome 1 | Chromosome 2 | ... | Chromosome 22 | Chromosome X | Chromosome Y
                choices: [valueCodeableConcept]
                index: 111
              valueCodeableConcept: {type: CodeableConcept, short: Chromosome 1 | Chromosome 2 | ... | Chromosome 22 | Chromosome X | Chromosome Y, choiceOf: value, index: 112}
            required: [value, valueCodeableConcept]
        representative-protein-hgvs:
          match: {}
          schema:
            short: Protein (Amino Acid) Change - pHGVS
            index: 113
            elements:
              code:
                short: 48005-3
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 48005-3, system: 'http://loinc.org'}
                index: 114
              value:
                short: A valid HGVS-formatted 'p.' string, e.g. NP_000050.2:p.(Asn1836Lys)
                choices: [valueCodeableConcept]
                index: 116
              valueCodeableConcept: {type: CodeableConcept, short: 'A valid HGVS-formatted ''p.'' string, e.g. NP_000050.2:p.(Asn1836Lys)', choiceOf: value, index: 117}
            required: [value, valueCodeableConcept]
        coordinate-system:
          match: {}
          schema:
            short: Coordinate System
            index: 52
            elements:
              code:
                short: 92822-6
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 92822-6, system: 'http://loinc.org'}
                index: 53
              value:
                short: 0-based interval counting | 0-based character counting | 1-based character counting
                choices: [valueCodeableConcept]
                index: 55
              valueCodeableConcept: {type: CodeableConcept, short: 0-based interval counting | 0-based character counting | 1-based character counting, choiceOf: value, index: 56}
            required: [value, valueCodeableConcept]
        coding-change-type:
          match: {}
          schema:
            short: Coding DNA Change Type
            index: 67
            elements:
              code:
                short: 48019-4
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 48019-4, system: 'http://loinc.org'}
                index: 68
              value:
                short: deletion | insertion | delins | SNV | copy_number_gain | copy_number_loss | ... (many)
                choices: [valueCodeableConcept]
                index: 70
              valueCodeableConcept: {type: CodeableConcept, short: deletion | insertion | delins | SNV | copy_number_gain | copy_number_loss | ... (many), choiceOf: value, index: 71}
            required: [value, valueCodeableConcept]
        repeat-motif:
          match: {}
          schema:
            short: Repeat Motif
            array: true
            index: 129
            extensions:
              repeat-motif-order: {url: 'http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order', min: 0, max: 1, type: Extension, index: 130}
            elements:
              extension:
                type: Extension
                url: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order
                index: 130
                slicing:
                  slices:
                    repeat-motif-order:
                      match: {}
                      schema: {type: Extension, url: 'http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order', index: 130}
                      min: 0
                      max: 1
              code:
                short: repeat-motif
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: repeat-motif, system: 'http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs'}
                index: 131
              value:
                short: CAG
                choices: [valueString]
                index: 133
              valueString: {type: string, short: CAG, choiceOf: value, index: 134}
            required: [valueString, value]
package_version: 3.0.0-ballot
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: 3.0.0-ballot