description: This cross-version extension represents MolecularSequence.variant from http://hl7.org/fhir/StructureDefinition/MolecularSequence|4.3.0 for use in FHIR R5.
package_name: hl7.fhir.uv.xver-r4b.r5
derivation: constraint
name: ext_R4B_MolecularSequence_variant
type: Extension
elements:
  extension:
    array: true
    index: 0
    slicing:
      rules: closed
      ordered: false
      discriminator:
      - {path: url, type: value}
      min: 0
      slices:
        start:
          match: {url: null}
          schema:
            isModifier: false
            short: Start position of the variant on the  reference sequence
            index: 1
            elements:
              value:
                base: {path: 'Extension.value[x]'}
                short: Start position of the variant on the  reference sequence
                choices: [valueInteger]
                index: 3
              valueInteger:
                base: {path: 'Extension.value[x]'}
                type: integer
                short: Start position of the variant on the  reference sequence
                choiceOf: value
                index: 4
        end:
          match: {url: null}
          schema:
            isModifier: false
            short: End position of the variant on the reference sequence
            index: 5
            elements:
              value:
                base: {path: 'Extension.value[x]'}
                short: End position of the variant on the reference sequence
                choices: [valueInteger]
                index: 7
              valueInteger:
                base: {path: 'Extension.value[x]'}
                type: integer
                short: End position of the variant on the reference sequence
                choiceOf: value
                index: 8
        observedAllele:
          match: {url: null}
          schema:
            isModifier: false
            short: Allele that was observed
            index: 9
            elements:
              value:
                base: {path: 'Extension.value[x]'}
                short: Allele that was observed
                choices: [valueString]
                index: 11
              valueString:
                base: {path: 'Extension.value[x]'}
                type: string
                short: Allele that was observed
                choiceOf: value
                index: 12
        referenceAllele:
          match: {url: null}
          schema:
            isModifier: false
            short: Allele in the reference sequence
            index: 13
            elements:
              value:
                base: {path: 'Extension.value[x]'}
                short: Allele in the reference sequence
                choices: [valueString]
                index: 15
              valueString:
                base: {path: 'Extension.value[x]'}
                type: string
                short: Allele in the reference sequence
                choiceOf: value
                index: 16
        cigar:
          match: {url: null}
          schema:
            isModifier: false
            short: Extended CIGAR string for aligning the sequence with reference bases
            index: 17
            elements:
              value:
                base: {path: 'Extension.value[x]'}
                short: Extended CIGAR string for aligning the sequence with reference bases
                choices: [valueString]
                index: 19
              valueString:
                base: {path: 'Extension.value[x]'}
                type: string
                short: Extended CIGAR string for aligning the sequence with reference bases
                choiceOf: value
                index: 20
        variantPointer:
          match: {url: null}
          schema:
            isModifier: false
            short: Pointer to observed variant information
            index: 21
            elements:
              value:
                base: {path: 'Extension.value[x]'}
                short: Pointer to observed variant information
                choices: [valueReference]
                index: 23
              valueReference:
                short: Pointer to observed variant information
                refers: ['http://hl7.org/fhir/StructureDefinition/Observation']
                type: Reference
                base: {path: 'Extension.value[x]'}
                choiceOf: value
                index: 24
  url:
    pattern: {type: Uri, value: 'http://hl7.org/fhir/4.3/StructureDefinition/extension-MolecularSequence.variant'}
    index: 25
package_version: 0.0.1-snapshot-1
extensions:
  start:
    url: null
    isModifier: false
    short: Start position of the variant on the  reference sequence
    index: 1
    elements:
      value:
        base: {path: 'Extension.value[x]'}
        short: Start position of the variant on the  reference sequence
        choices: [valueInteger]
        index: 3
      valueInteger:
        base: {path: 'Extension.value[x]'}
        type: integer
        short: Start position of the variant on the  reference sequence
        choiceOf: value
        index: 4
  end:
    url: null
    isModifier: false
    short: End position of the variant on the reference sequence
    index: 5
    elements:
      value:
        base: {path: 'Extension.value[x]'}
        short: End position of the variant on the reference sequence
        choices: [valueInteger]
        index: 7
      valueInteger:
        base: {path: 'Extension.value[x]'}
        type: integer
        short: End position of the variant on the reference sequence
        choiceOf: value
        index: 8
  observedAllele:
    url: null
    isModifier: false
    short: Allele that was observed
    index: 9
    elements:
      value:
        base: {path: 'Extension.value[x]'}
        short: Allele that was observed
        choices: [valueString]
        index: 11
      valueString:
        base: {path: 'Extension.value[x]'}
        type: string
        short: Allele that was observed
        choiceOf: value
        index: 12
  referenceAllele:
    url: null
    isModifier: false
    short: Allele in the reference sequence
    index: 13
    elements:
      value:
        base: {path: 'Extension.value[x]'}
        short: Allele in the reference sequence
        choices: [valueString]
        index: 15
      valueString:
        base: {path: 'Extension.value[x]'}
        type: string
        short: Allele in the reference sequence
        choiceOf: value
        index: 16
  cigar:
    url: null
    isModifier: false
    short: Extended CIGAR string for aligning the sequence with reference bases
    index: 17
    elements:
      value:
        base: {path: 'Extension.value[x]'}
        short: Extended CIGAR string for aligning the sequence with reference bases
        choices: [valueString]
        index: 19
      valueString:
        base: {path: 'Extension.value[x]'}
        type: string
        short: Extended CIGAR string for aligning the sequence with reference bases
        choiceOf: value
        index: 20
  variantPointer:
    url: null
    isModifier: false
    short: Pointer to observed variant information
    index: 21
    elements:
      value:
        base: {path: 'Extension.value[x]'}
        short: Pointer to observed variant information
        choices: [valueReference]
        index: 23
      valueReference:
        short: Pointer to observed variant information
        refers: ['http://hl7.org/fhir/StructureDefinition/Observation']
        type: Reference
        base: {path: 'Extension.value[x]'}
        choiceOf: value
        index: 24
class: extension
kind: complex-type
url: http://hl7.org/fhir/4.3/StructureDefinition/extension-MolecularSequence.variant
base: http://hl7.org/fhir/StructureDefinition/Extension
version: 0.0.1-snapshot-1
required: [url]