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:
    pattern:
      type: CodeableConcept
      value:
        coding:
        - {code: 69548-6, system: 'http://loinc.org'}
    index: 0
  valueCodeableConcept:
    type: CodeableConcept
    binding: {strength: required, valueSet: 'http://loinc.org/vs/LL1971-2'}
    index: 1
  method:
    binding: {strength: extensible, valueSet: 'http://loinc.org/vs/LL4048-6'}
    index: 2
  component:
    short: DNA Change - Transcript (cHGVS)
    index: 3
    slicing:
      slices:
        alt-allele:
          match: {}
          schema:
            short: Genomic alt allele
            index: 79
            elements:
              code:
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 69551-0, system: 'http://loinc.org'}
                index: 80
              value:
                choices: [valueString]
                index: 82
              valueString: {type: string, choiceOf: value, index: 83}
        allelic-state:
          match: {}
          schema:
            short: Allelic state
            index: 64
            elements:
              code:
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 53034-5, system: 'http://loinc.org'}
                index: 65
              value:
                choices: [valueCodeableConcept]
                index: 67
              valueCodeableConcept: {type: CodeableConcept, choiceOf: value, index: 68}
            required: [value, valueCodeableConcept]
        molecular-consequence:
          match: {}
          schema:
            short: Molecular Consequence
            index: 13
            elements:
              code:
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: molecular-consequence, system: 'http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/TbdCodes'}
                index: 14
              value:
                short: Concepts in sequence ontology under SO:0001537 (see http://www.sequenceontology.org/browser/current_release/term/SO:0001537).
                choices: [valueCodeableConcept]
                index: 16
              valueCodeableConcept: {type: CodeableConcept, short: 'Concepts in sequence ontology under SO:0001537 (see http://www.sequenceontology.org/browser/current_release/term/SO:0001537).', choiceOf: value, index: 17}
            required: [value, valueCodeableConcept]
        allelic-read-depth:
          match: {}
          schema:
            short: Allelic read depth
            index: 59
            elements:
              code:
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 82121-5, system: 'http://loinc.org'}
                index: 60
              value:
                choices: [valueQuantity]
                index: 62
              valueQuantity: {type: Quantity, choiceOf: value, index: 63}
        outer-start-end:
          match: {}
          schema:
            short: Variant outer start and end
            index: 94
            elements:
              code:
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: outer-start-end, system: 'http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/TbdCodes'}
                index: 95
              value:
                choices: [valueRange]
                index: 97
              valueRange: {type: Range, choiceOf: value, index: 98}
        genomic-source-class:
          match: {}
          schema:
            short: Genomic Source Class
            index: 28
            elements:
              code:
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 48002-0, system: 'http://loinc.org'}
                index: 29
              value:
                choices: [valueCodeableConcept]
                index: 31
              valueCodeableConcept: {type: CodeableConcept, choiceOf: value, index: 32}
            required: [value, valueCodeableConcept]
        copy-number:
          match: {}
          schema:
            short: Genomic structural variant copy number
            index: 69
            elements:
              code:
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 82155-3, system: 'http://loinc.org'}
                index: 70
              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: 72
              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: 73
        amino-acid-chg-type:
          match: {}
          schema:
            short: Amino acid change type
            index: 38
            elements:
              code:
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 48006-1, system: 'http://loinc.org'}
                index: 39
              value:
                choices: [valueCodeableConcept]
                index: 41
              valueCodeableConcept: {type: CodeableConcept, choiceOf: value, index: 42}
            required: [value, valueCodeableConcept]
        variation-code:
          match: {}
          schema:
            short: Variation Code
            index: 18
            elements:
              code:
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 81252-9, system: 'http://loinc.org'}
                index: 19
              value:
                choices: [valueCodeableConcept]
                index: 21
              valueCodeableConcept: {type: CodeableConcept, choiceOf: value, index: 22}
            required: [value, valueCodeableConcept]
        exact-start-end:
          match: {}
          schema:
            short: Exact start-end
            index: 89
            elements:
              code:
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: exact-start-end, system: 'http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/TbdCodes'}
                index: 90
              value:
                choices: [valueRange]
                index: 92
              valueRange: {type: Range, choiceOf: value, index: 93}
        ref-allele:
          match: {}
          schema:
            short: Genomic ref allele
            index: 74
            elements:
              code:
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 69547-8, system: 'http://loinc.org'}
                index: 75
              value:
                choices: [valueString]
                index: 77
              valueString: {type: string, choiceOf: value, index: 78}
        genomic-dna-chg:
          match: {}
          schema:
            short: DNA Change - Genomic (gHGVS)
            index: 23
            elements:
              code:
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 81290-9, system: 'http://loinc.org'}
                index: 24
              value:
                choices: [valueCodeableConcept]
                index: 26
              valueCodeableConcept: {type: CodeableConcept, choiceOf: value, index: 27}
            required: [value, valueCodeableConcept]
        amino-acid-chg:
          match: {}
          schema:
            short: Amino acid change (pHGVS)
            index: 33
            elements:
              code:
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 48005-3, system: 'http://loinc.org'}
                index: 34
              value:
                choices: [valueCodeableConcept]
                index: 36
              valueCodeableConcept: {type: CodeableConcept, choiceOf: value, index: 37}
            required: [value, valueCodeableConcept]
        inner-start-end:
          match: {}
          schema:
            short: Variant inner start and end
            index: 99
            elements:
              code:
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: inner-start-end, system: 'http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/TbdCodes'}
                index: 100
              value:
                choices: [valueRange]
                index: 102
              valueRange: {type: Range, choiceOf: value, index: 103}
        transcript-ref-seq:
          match: {}
          schema:
            short: Transcript reference sequence ID
            index: 43
            elements:
              code:
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 51958-7, system: 'http://loinc.org'}
                index: 44
              value:
                choices: [valueCodeableConcept]
                index: 46
              valueCodeableConcept: {type: CodeableConcept, choiceOf: value, index: 47}
            required: [value, valueCodeableConcept]
        dna-chg:
          match: {}
          schema:
            short: DNA Change - Transcript (cHGVS)
            index: 3
            elements:
              code:
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 48004-6, system: 'http://loinc.org'}
                index: 4
              value:
                choices: [valueCodeableConcept]
                index: 6
              valueCodeableConcept: {type: CodeableConcept, choiceOf: value, index: 7}
            required: [value, valueCodeableConcept]
        sample-allelic-frequency:
          match: {}
          schema:
            short: Sample Allelic Frequency
            index: 53
            elements:
              code:
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 81258-6, system: 'http://loinc.org'}
                index: 54
              value:
                choices: [valueQuantity]
                index: 56
              valueQuantity: {type: Quantity, choiceOf: value, index: 57}
              value[x]:
                elements:
                  system:
                    pattern: {type: Uri, value: 'http://unitsofmeasure.org'}
                    index: 58
        genomic-ref-seq:
          match: {}
          schema:
            short: Genomic reference sequence ID
            index: 48
            elements:
              code:
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 48013-7, system: 'http://loinc.org'}
                index: 49
              value:
                choices: [valueCodeableConcept]
                index: 51
              valueCodeableConcept: {type: CodeableConcept, choiceOf: value, index: 52}
            required: [value, valueCodeableConcept]
        cytogenomic-nomenclature:
          match: {}
          schema:
            short: Cytogenomic Nomenclature
            index: 104
            elements:
              code:
                short: Variant ISCN
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 81291-7, system: 'http://loinc.org'}
                index: 105
              value:
                choices: [valueCodeableConcept]
                index: 107
              valueCodeableConcept: {type: CodeableConcept, choiceOf: value, index: 108}
            required: [value, valueCodeableConcept]
        variant-inheritance:
          match: {}
          schema:
            short: Variant Inheritance
            index: 109
            elements:
              code:
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: variant-inheritance, system: 'http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/TbdCodes'}
                index: 110
              value:
                choices: [valueCodeableConcept]
                index: 112
              valueCodeableConcept: {type: CodeableConcept, choiceOf: value, index: 113}
            required: [value, valueCodeableConcept]
        chromosome-identifier:
          match: {}
          schema:
            short: Chromosome Identifier
            array: true
            index: 114
            elements:
              code:
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 48000-4, system: 'http://loinc.org'}
                index: 115
              value:
                choices: [valueCodeableConcept]
                index: 117
              valueCodeableConcept: {type: CodeableConcept, choiceOf: value, index: 118}
            required: [value, valueCodeableConcept]
        dna-chg-type:
          match: {}
          schema:
            short: DNA Change Type
            index: 8
            elements:
              code:
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 48019-4, system: 'http://loinc.org'}
                index: 9
              value:
                short: Concepts in sequence ontology under SO:0002072 (see http://www.sequenceontology.org/browser/current_release/term/SO:0002072).
                choices: [valueCodeableConcept]
                index: 11
              valueCodeableConcept: {type: CodeableConcept, short: 'Concepts in sequence ontology under SO:0002072 (see http://www.sequenceontology.org/browser/current_release/term/SO:0002072).', choiceOf: value, index: 12}
            required: [value, valueCodeableConcept]
        coordinate-system:
          match: {}
          schema:
            short: Coordinate System
            index: 84
            elements:
              code:
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 92822-6, system: 'http://loinc.org'}
                index: 85
              value:
                choices: [valueCodeableConcept]
                index: 87
              valueCodeableConcept: {type: CodeableConcept, choiceOf: value, index: 88}
            required: [value, valueCodeableConcept]
package_version: reporting-1.1.0
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: 1.1.0