description: Details about a set of changes in the tested sample compared to a reference 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:
  category:
    mustSupport: true
    index: 1
    slicing:
      slices:
        labCategory:
          match: {}
          schema:
            pattern:
              type: CodeableConcept
              value:
                coding:
                - {code: laboratory, system: 'http://terminology.hl7.org/CodeSystem/observation-category'}
            index: 2
            elements:
              coding: {index: 3}
  referenceRange: {short: Not used in this profile, index: 14}
  hasMember: {short: Not used in this profile, index: 15}
  method: {mustSupport: true, index: 12}
  specimen:
    type: Reference
    mustSupport: true
    refers: ['http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-human-specimen']
    index: 13
  value:
    mustSupport: true
    choices: []
    index: 10
  component:
    mustSupport: true
    index: 16
    slicing:
      slices:
        allelic-state:
          match: {}
          schema:
            mustSupport: true
            index: 45
            elements:
              code: {mustSupport: true, index: 46}
              value:
                mustSupport: true
                choices: []
                index: 48
        molecular-consequence:
          match: {}
          schema:
            mustSupport: true
            index: 61
            elements:
              code: {mustSupport: true, index: 62}
              value:
                mustSupport: true
                choices: []
                index: 64
        genomic-source-class:
          match: {}
          schema:
            mustSupport: true
            index: 37
            elements:
              code: {mustSupport: true, index: 38}
              value:
                mustSupport: true
                choices: []
                index: 40
        copy-number:
          match: {}
          schema:
            mustSupport: true
            index: 65
            elements:
              code: {mustSupport: true, index: 66}
              value:
                mustSupport: true
                choices: []
                index: 68
        variation-code:
          match: {}
          schema:
            mustSupport: true
            index: 49
            elements:
              code: {mustSupport: true, index: 50}
              value:
                mustSupport: true
                choices: []
                index: 52
        genomic-hgvs:
          match: {}
          schema:
            mustSupport: true
            index: 25
            elements:
              code: {mustSupport: true, index: 26}
              value:
                mustSupport: true
                choices: []
                index: 28
        amino-acid-change-type:
          match: {}
          schema:
            mustSupport: true
            index: 57
            elements:
              code: {mustSupport: true, index: 58}
              value:
                mustSupport: true
                choices: []
                index: 60
        cytogenetic-location:
          match: {}
          schema:
            mustSupport: true
            index: 21
            elements:
              code: {mustSupport: true, index: 22}
              value:
                mustSupport: true
                choices: []
                index: 24
        sample-allelic-frequency:
          match: {}
          schema:
            mustSupport: true
            index: 41
            elements:
              code: {mustSupport: true, index: 42}
              value:
                mustSupport: true
                choices: []
                index: 44
        protein-hgvs:
          match: {}
          schema:
            mustSupport: true
            index: 53
            elements:
              code: {mustSupport: true, index: 54}
              value:
                mustSupport: true
                choices: []
                index: 56
        cytogenomic-nomenclature:
          match: {}
          schema:
            mustSupport: true
            index: 29
            elements:
              code: {mustSupport: true, index: 30}
              value:
                mustSupport: true
                choices: []
                index: 32
        gene-studied:
          match: {}
          schema:
            mustSupport: true
            index: 17
            elements:
              code: {mustSupport: true, index: 18}
              value:
                mustSupport: true
                choices: []
                index: 20
        coding-change-type:
          match: {}
          schema:
            mustSupport: true
            index: 33
            elements:
              code: {mustSupport: true, index: 34}
              value:
                mustSupport: true
                choices: []
                index: 36
  effectiveDateTime: {type: dateTime, mustSupport: true, index: 8}
  status: {mustSupport: true, index: 0}
  effective:
    mustSupport: true
    choices: []
    index: 7
  code: {mustSupport: true, index: 4}
  subject:
    type: Reference
    mustSupport: true
    refers: ['http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-cancer-patient']
    index: 5
  dataAbsentReason: {mustSupport: true, index: 11}
package_version: 3.0.0-ballot
class: profile
kind: resource
url: http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-genomic-variant
base: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant
version: 3.0.0-ballot