description: An alteration in the most common DNA nucleotide sequence. The term variant can be used to describe an alteration that may be benign, pathogenic, or of unknown significance. The term variant is increasingly being used in place of the term mutation. Variants can be computed relative to reference sequence assembly from which it was identified.
package_name: hl7.fhir.us.mcode
derivation: constraint
name: GenomicVariant
type: Observation
elements:
  referenceRange: {short: Not used in this profile, index: 7}
  hasMember: {short: Not used in this profile, index: 8}
  method:
    binding: {strength: extensible, valueSet: 'http://loinc.org/vs/LL4048-6'}
    mustSupport: true
    index: 5
  specimen:
    type: Reference
    mustSupport: true
    refers: ['http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-genomic-specimen']
    index: 6
  value:
    short: Whether the variant is present
    choices: [valueCodeableConcept]
    index: 2
  component:
    mustSupport: true
    index: 9
    elements:
      code: {mustSupport: true, index: 10}
      value:
        mustSupport: true
        choices: []
        index: 12
    slicing:
      rules: open
      description: Slice based on the component.code pattern
      discriminator:
      - {path: code, type: pattern}
      min: null
      slices:
        genomicDNAChangeType:
          match:
            code:
              coding:
              - {code: 48019-4, system: 'http://loinc.org'}
          schema:
            short: DNA Change Type
            mustSupport: true
            index: 28
            elements:
              code:
                mustSupport: true
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 48019-4, system: 'http://loinc.org'}
                index: 29
              value:
                mustSupport: true
                choices: [valueCodeableConcept]
                index: 31
              valueCodeableConcept: {type: CodeableConcept, mustSupport: true, choiceOf: value, index: 32}
        variationCode:
          match:
            code:
              coding:
              - {code: 81252-9, system: 'http://loinc.org'}
          schema:
            short: Discrete Genomic variant
            mustSupport: true
            index: 18
            elements:
              code:
                mustSupport: true
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 81252-9, system: 'http://loinc.org'}
                index: 19
              value:
                mustSupport: true
                choices: [valueCodeableConcept]
                index: 21
              valueCodeableConcept: {type: CodeableConcept, mustSupport: true, choiceOf: value, index: 22}
        molecularConsequence:
          match:
            code:
              coding:
              - {code: molecular-consequence, system: 'http://hl7.org/fhir/us/mcode/CodeSystem/loinc-requested-cs'}
          schema:
            short: Molecular consequence
            mustSupport: true
            index: 33
            elements:
              code:
                mustSupport: true
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: molecular-consequence, system: 'http://hl7.org/fhir/us/mcode/CodeSystem/loinc-requested-cs'}
                index: 34
              value:
                mustSupport: true
                choices: [valueCodeableConcept]
                index: 36
              valueCodeableConcept: {type: CodeableConcept, mustSupport: true, choiceOf: value, index: 37}
        aminoAcidChangeType:
          match:
            code:
              coding:
              - {code: 48006-1, system: 'http://loinc.org'}
          schema:
            short: Amino acid change [Type]
            mustSupport: true
            index: 48
            elements:
              code:
                mustSupport: true
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 48006-1, system: 'http://loinc.org'}
                index: 49
              value:
                mustSupport: true
                choices: [valueCodeableConcept]
                index: 51
              valueCodeableConcept: {type: CodeableConcept, mustSupport: true, choiceOf: value, index: 52}
        cytogeneticLocation:
          match:
            code:
              coding:
              - {code: 48001-2, system: 'http://loinc.org'}
          schema:
            short: Cytogenetic (chromosome) location
            mustSupport: true
            array: true
            index: 68
            elements:
              code:
                mustSupport: true
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 48001-2, system: 'http://loinc.org'}
                index: 69
              value:
                mustSupport: true
                choices: []
                index: 71
        clinicalSignificance:
          match:
            code:
              coding:
              - {code: 53037-8, system: 'http://loinc.org'}
          schema:
            short: Genomic variation clinical significance [Imp]
            mustSupport: true
            index: 76
            elements:
              code:
                mustSupport: true
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 53037-8, system: 'http://loinc.org'}
                index: 77
              value:
                mustSupport: true
                choices: [valueCodeableConcept]
                index: 79
              valueCodeableConcept: {type: CodeableConcept, mustSupport: true, choiceOf: value, index: 80}
        cytogeneticNomenclature:
          match:
            code:
              coding:
              - {code: 81291-7, system: 'http://loinc.org'}
          schema:
            short: Variant ISCN
            mustSupport: true
            array: true
            index: 72
            elements:
              code:
                mustSupport: true
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 81291-7, system: 'http://loinc.org'}
                index: 73
              value:
                mustSupport: true
                choices: []
                index: 75
        aminoAcidChange:
          match:
            code:
              coding:
              - {code: 48005-3, system: 'http://loinc.org'}
          schema:
            short: Amino acid change (pHGVS)
            mustSupport: true
            index: 43
            elements:
              code:
                mustSupport: true
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 48005-3, system: 'http://loinc.org'}
                index: 44
              value:
                mustSupport: true
                choices: [valueCodeableConcept]
                index: 46
              valueCodeableConcept: {type: CodeableConcept, mustSupport: true, choiceOf: value, index: 47}
        genomicSourceClass:
          match:
            code:
              coding:
              - {code: 48002-0, system: 'http://loinc.org'}
          schema:
            short: Genomic source class [Type]
            mustSupport: true
            index: 38
            elements:
              code:
                mustSupport: true
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 48002-0, system: 'http://loinc.org'}
                index: 39
              value:
                mustSupport: true
                choices: [valueCodeableConcept]
                index: 41
              valueCodeableConcept: {type: CodeableConcept, mustSupport: true, choiceOf: value, index: 42}
        allelicState:
          match:
            code:
              coding:
              - {code: 53034-5, system: 'http://loinc.org'}
          schema:
            short: sample allelic frequency
            mustSupport: true
            index: 63
            elements:
              code:
                mustSupport: true
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 53034-5, system: 'http://loinc.org'}
                index: 64
              value:
                mustSupport: true
                choices: [valueCodeableConcept]
                index: 66
              valueCodeableConcept: {type: CodeableConcept, mustSupport: true, choiceOf: value, index: 67}
        copyNumber:
          match:
            code:
              coding:
              - {code: 82155-3, system: 'http://loinc.org'}
          schema:
            short: Genomic structural variant copy number
            mustSupport: true
            index: 53
            elements:
              code:
                mustSupport: true
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 82155-3, system: 'http://loinc.org'}
                index: 54
              value:
                mustSupport: true
                choices: [valueQuantity]
                index: 56
              valueQuantity: {type: Quantity, mustSupport: true, choiceOf: value, index: 57}
        geneStudied:
          match:
            code:
              coding:
              - {code: 48018-6, system: 'http://loinc.org'}
          schema:
            short: Gene studied [ID]
            mustSupport: true
            array: true
            index: 13
            elements:
              code:
                mustSupport: true
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 48018-6, system: 'http://loinc.org'}
                index: 14
              value:
                mustSupport: true
                choices: [valueCodeableConcept]
                index: 16
              valueCodeableConcept: {type: CodeableConcept, mustSupport: true, choiceOf: value, index: 17}
        sampleAllelicFrequency:
          match:
            code:
              coding:
              - {code: 81258-6, system: 'http://loinc.org'}
          schema:
            short: sample allelic frequency
            mustSupport: true
            index: 58
            elements:
              code:
                mustSupport: true
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 81258-6, system: 'http://loinc.org'}
                index: 59
              value:
                mustSupport: true
                choices: [valueQuantity]
                index: 61
              valueQuantity: {type: Quantity, mustSupport: true, choiceOf: value, index: 62}
        genomicDNAChange:
          match:
            code:
              coding:
              - {code: 81290-9, system: 'http://loinc.org'}
          schema:
            short: Genomic DNA change (gHGVS)
            mustSupport: true
            index: 23
            elements:
              code:
                mustSupport: true
                pattern:
                  type: CodeableConcept
                  value:
                    coding:
                    - {code: 81290-9, system: 'http://loinc.org'}
                index: 24
              value:
                mustSupport: true
                choices: [valueCodeableConcept]
                index: 26
              valueCodeableConcept: {type: CodeableConcept, mustSupport: true, choiceOf: value, index: 27}
  code:
    pattern:
      type: CodeableConcept
      value:
        coding:
        - {code: 69548-6, system: 'http://loinc.org'}
    index: 0
  valueCodeableConcept: {type: CodeableConcept, short: Whether the variant is present, choiceOf: value, index: 3}
  bodySite: {short: Not used in this profile, index: 4}
package_version: 2.0.0
class: profile
kind: resource
url: http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-genomic-variant
base: http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-lab
version: 2.0.0