description: Details about a set of changes in the tested sample compared to a reference sequence.
package_name: hl7.fhir.uv.genomics
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
  valueCodeableConcept:
    type: CodeableConcept
    short: Indeterminate | No call | Present | Absent.
    binding: {strength: required, valueSet: 'http://loinc.org/vs/LL1971-2'}
    index: 1
  method:
    short: Sequencing | SNP array | PCR | Computational analysis | ...
    binding: {strength: extensible, valueSet: 'http://loinc.org/vs/LL4048-6'}
    index: 2
  component:
    short: Coding (cDNA) Change - cHGVS
    index: 3
    slicing:
      slices:
        alt-allele:
          match: {}
          schema:
            short: Genomic Alt Allele
            index: 53
            elements:
              code:
                short: 69551-0
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 69551-0, system: 'http://loinc.org'}
                index: 54
              value:
                short: Normalized string per the VCF format.
                choices: [valueString]
                index: 56
              valueString: {type: string, short: Normalized string per the VCF format., choiceOf: value, index: 57}
        allelic-state:
          match: {}
          schema:
            short: Allelic State
            index: 79
            elements:
              code:
                short: 53034-5
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 53034-5, system: 'http://loinc.org'}
                index: 80
              value:
                short: Heteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous
                choices: [valueCodeableConcept]
                index: 82
              valueCodeableConcept: {type: CodeableConcept, short: Heteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous, choiceOf: value, index: 83}
            required: [value, valueCodeableConcept]
        molecular-consequence:
          match: {}
          schema:
            short: Molecular Consequence
            index: 109
            elements:
              code:
                short: molecular-consequence
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: molecular-consequence, system: 'http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs'}
                index: 110
              value:
                short: stop_lost | stop_gained | inframe_insertion | frameshift_variant | ... (many)
                choices: [valueCodeableConcept]
                index: 112
              valueCodeableConcept: {type: CodeableConcept, short: stop_lost | stop_gained | inframe_insertion | frameshift_variant | ... (many), choiceOf: value, index: 113}
            required: [value, valueCodeableConcept]
        allelic-read-depth:
          match: {}
          schema:
            short: Allelic Read Depth
            index: 74
            elements:
              code:
                short: 82121-5
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 82121-5, system: 'http://loinc.org'}
                index: 75
              value:
                short: Unfiltered count of supporting reads
                choices: [valueQuantity]
                index: 77
              valueQuantity: {type: Quantity, short: Unfiltered count of supporting reads, choiceOf: value, index: 78}
        outer-start-end:
          match: {}
          schema:
            short: Outer Start-End
            index: 38
            elements:
              code:
                short: 81301-4
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 81301-4, system: 'http://loinc.org'}
                index: 39
              value:
                short: Imprecise variant outer-bounding range
                choices: [valueRange]
                index: 41
              valueRange: {type: Range, short: Imprecise variant outer-bounding range, choiceOf: value, index: 42}
        coding-hgvs:
          match: {}
          schema:
            short: Coding (cDNA) Change - cHGVS
            index: 3
            elements:
              code:
                short: 48004-6
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 48004-6, system: 'http://loinc.org'}
                index: 4
              value:
                short: A valid HGVS-formatted 'c.' string, e.g. NM_005228.5:c.2369C>T.
                choices: [valueCodeableConcept]
                index: 6
              valueCodeableConcept: {type: CodeableConcept, short: 'A valid HGVS-formatted ''c.'' string, e.g. NM_005228.5:c.2369C>T.', choiceOf: value, index: 7}
            required: [value, valueCodeableConcept]
        genomic-source-class:
          match: {}
          schema:
            short: Genomic Source Class
            index: 63
            elements:
              code:
                short: 48002-0
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 48002-0, system: 'http://loinc.org'}
                index: 64
              value:
                short: Germline | Somatic | Fetal | Likely germline | Likely somatic | Likely fetal | Unknown genomic origin | De novo
                choices: [valueCodeableConcept]
                index: 66
              valueCodeableConcept: {type: CodeableConcept, short: Germline | Somatic | Fetal | Likely germline | Likely somatic | Likely fetal | Unknown genomic origin | De novo, choiceOf: value, index: 67}
            required: [value, valueCodeableConcept]
        copy-number:
          match: {}
          schema:
            short: Genomic Structural Variant Copy Number
            index: 114
            elements:
              code:
                short: 82155-3
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 82155-3, system: 'http://loinc.org'}
                index: 115
              value:
                constraint:
                  cnt-3: {human: 'There SHALL be a code with a value of ''1'' if there is a value. If system is present, it SHALL be UCUM. If present, the value SHALL be a whole number.', source: 'http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant', severity: error, expression: (code.exists() or value.empty()) and (system.empty() or system = %ucum) and (code.empty() or code = '1') and (value.empty() or value.hasValue().not() or value.toString().contains('.').not())}
                choices: [valueQuantity]
                index: 117
              valueQuantity:
                type: Quantity
                constraint:
                  cnt-3: {human: 'There SHALL be a code with a value of ''1'' if there is a value. If system is present, it SHALL be UCUM. If present, the value SHALL be a whole number.', source: 'http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant', severity: error, expression: (code.exists() or value.empty()) and (system.empty() or system = %ucum) and (code.empty() or code = '1') and (value.empty() or value.hasValue().not() or value.toString().contains('.').not())}
                choiceOf: value
                index: 118
        variation-code:
          match: {}
          schema:
            short: Variation Code
            array: true
            index: 89
            elements:
              code:
                short: 81252-9
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 81252-9, system: 'http://loinc.org'}
                index: 90
              value:
                short: ClinVar ID or similar
                choices: [valueCodeableConcept]
                index: 92
              valueCodeableConcept: {type: CodeableConcept, short: ClinVar ID or similar, choiceOf: value, index: 93}
            required: [value, valueCodeableConcept]
        exact-start-end:
          match: {}
          schema:
            short: Exact Start-End
            index: 28
            elements:
              code:
                short: 81254-5
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 81254-5, system: 'http://loinc.org'}
                index: 29
              value:
                short: Range in question. 'High' can be omitted for single nucleotide variants.
                choices: [valueRange]
                index: 31
              valueRange: {type: Range, short: Range in question. 'High' can be omitted for single nucleotide variants., choiceOf: value, index: 32}
        genomic-hgvs:
          match: {}
          schema:
            short: Genomic (gDNA) Change - gHGVS
            index: 8
            elements:
              code:
                short: 81290-9
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 81290-9, system: 'http://loinc.org'}
                index: 9
              value:
                short: A valid HGVS-formatted 'g.' string, e.g. NC_000016.9:g.2124200_2138612dup
                choices: [valueCodeableConcept]
                index: 11
              valueCodeableConcept: {type: CodeableConcept, short: 'A valid HGVS-formatted ''g.'' string, e.g. NC_000016.9:g.2124200_2138612dup', choiceOf: value, index: 12}
            required: [value, valueCodeableConcept]
        ref-allele:
          match: {}
          schema:
            short: Genomic Ref Allele
            index: 48
            elements:
              code:
                short: 69547-8
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 69547-8, system: 'http://loinc.org'}
                index: 49
              value:
                short: Normalized string per the VCF format.
                choices: [valueString]
                index: 51
              valueString: {type: string, short: Normalized string per the VCF format., choiceOf: value, index: 52}
        inner-start-end:
          match: {}
          schema:
            short: Inner Start-End
            index: 33
            elements:
              code:
                short: 81302-2
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 81302-2, system: 'http://loinc.org'}
                index: 34
              value:
                short: Imprecise variant inner-bounding range
                choices: [valueRange]
                index: 36
              valueRange: {type: Range, short: Imprecise variant inner-bounding range, choiceOf: value, index: 37}
        amino-acid-change-type:
          match: {}
          schema:
            short: Amino Acid Change Type
            index: 104
            elements:
              code:
                short: 48006-1
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 48006-1, system: 'http://loinc.org'}
                index: 105
              value:
                short: Wild type | Deletion | Duplication | Frameshift | Initiating Methionine | Insertion | Insertion and Deletion | Missense | Nonsense | Silent
                choices: [valueCodeableConcept]
                index: 107
              valueCodeableConcept: {type: CodeableConcept, short: Wild type | Deletion | Duplication | Frameshift | Initiating Methionine | Insertion | Insertion and Deletion | Missense | Nonsense | Silent, choiceOf: value, index: 108}
            required: [value, valueCodeableConcept]
        variant-confidence-status:
          match: {}
          schema:
            short: Variant Confidence Status
            index: 119
            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: 120
              value:
                short: High | Intermediate | Low
                choices: [valueCodeableConcept]
                index: 122
              valueCodeableConcept: {type: CodeableConcept, short: High | Intermediate | Low, choiceOf: value, index: 123}
            required: [value, valueCodeableConcept]
        transcript-ref-seq:
          match: {}
          schema:
            short: Reference Transcript
            index: 23
            elements:
              code:
                short: 51958-7
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 51958-7, system: 'http://loinc.org'}
                index: 24
              value:
                short: Versioned transcript reference sequence identifier
                choices: [valueCodeableConcept]
                index: 26
              valueCodeableConcept: {type: CodeableConcept, short: Versioned transcript reference sequence identifier, choiceOf: value, index: 27}
            required: [value, valueCodeableConcept]
        sample-allelic-frequency:
          match: {}
          schema:
            short: Sample Allelic Frequency
            index: 68
            elements:
              code:
                short: 81258-6
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 81258-6, system: 'http://loinc.org'}
                index: 69
              value:
                short: Relative frequency in the sample
                choices: [valueQuantity]
                index: 71
              valueQuantity: {type: Quantity, short: Relative frequency in the sample, choiceOf: value, index: 72}
              value[x]:
                elements:
                  system:
                    pattern: {type: Uri, value: 'http://unitsofmeasure.org'}
                    index: 73
        protein-hgvs:
          match: {}
          schema:
            short: Protein (Amino Acid) Change - pHGVS
            index: 99
            elements:
              code:
                short: 48005-3
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 48005-3, system: 'http://loinc.org'}
                index: 100
              value:
                short: A valid HGVS-formatted 'p.' string, e.g. NP_000050.2:p.(Asn1836Lys)
                choices: [valueCodeableConcept]
                index: 102
              valueCodeableConcept: {type: CodeableConcept, short: 'A valid HGVS-formatted ''p.'' string, e.g. NP_000050.2:p.(Asn1836Lys)', choiceOf: value, index: 103}
            required: [value, valueCodeableConcept]
        genomic-ref-seq:
          match: {}
          schema:
            short: Genomic Reference Sequence
            index: 18
            elements:
              code:
                short: 48013-7
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 48013-7, system: 'http://loinc.org'}
                index: 19
              value:
                short: Versioned genomic reference sequence identifier
                choices: [valueCodeableConcept]
                index: 21
              valueCodeableConcept: {type: CodeableConcept, short: Versioned genomic reference sequence identifier, choiceOf: value, index: 22}
            required: [value, valueCodeableConcept]
        cytogenomic-nomenclature:
          match: {}
          schema:
            short: Cytogenomic Nomenclature (ISCN)
            index: 13
            elements:
              code:
                short: 81291-7
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 81291-7, system: 'http://loinc.org'}
                index: 14
              value:
                choices: [valueCodeableConcept]
                index: 16
              valueCodeableConcept: {type: CodeableConcept, choiceOf: value, index: 17}
            required: [value, valueCodeableConcept]
        variant-inheritance:
          match: {}
          schema:
            short: Variant Inheritance
            index: 84
            elements:
              code:
                short: variant-inheritance
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: variant-inheritance, system: 'http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs'}
                index: 85
              value:
                short: Maternal | Paternal | Unknown
                choices: [valueCodeableConcept]
                index: 87
              valueCodeableConcept: {type: CodeableConcept, short: Maternal | Paternal | Unknown, choiceOf: value, index: 88}
            required: [value, valueCodeableConcept]
        chromosome-identifier:
          match: {}
          schema:
            short: Chromosome Identifier
            array: true
            index: 94
            elements:
              code:
                short: 48000-4
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 48000-4, system: 'http://loinc.org'}
                index: 95
              value:
                short: Chromosome 1 | Chromosome 2 | ... | Chromosome 22 | Chromosome X | Chromosome Y
                choices: [valueCodeableConcept]
                index: 97
              valueCodeableConcept: {type: CodeableConcept, short: Chromosome 1 | Chromosome 2 | ... | Chromosome 22 | Chromosome X | Chromosome Y, choiceOf: value, index: 98}
            required: [value, valueCodeableConcept]
        coordinate-system:
          match: {}
          schema:
            short: Coordinate System
            index: 43
            elements:
              code:
                short: 92822-6
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 92822-6, system: 'http://loinc.org'}
                index: 44
              value:
                short: 0-based interval counting | 0-based character counting | 1-based character counting
                choices: [valueCodeableConcept]
                index: 46
              valueCodeableConcept: {type: CodeableConcept, short: 0-based interval counting | 0-based character counting | 1-based character counting, choiceOf: value, index: 47}
            required: [value, valueCodeableConcept]
        coding-change-type:
          match: {}
          schema:
            short: Coding DNA Change Type
            index: 58
            elements:
              code:
                short: 48019-4
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 48019-4, system: 'http://loinc.org'}
                index: 59
              value:
                short: deletion | insertion | delins | SNV | copy_number_gain | copy_number_loss | ... (many)
                choices: [valueCodeableConcept]
                index: 61
              valueCodeableConcept: {type: CodeableConcept, short: deletion | insertion | delins | SNV | copy_number_gain | copy_number_loss | ... (many), choiceOf: value, index: 62}
            required: [value, valueCodeableConcept]
package_version: reporting-2.0.0
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: 2.0.0