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FHIR IG analytics

Packagepc.ig
Resource TypeBasic
IdBasic-variant-annotation-example-1.json
FHIR VersionR4

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Narrative

Note: links and images are rebased to the (stated) source

Generated Narrative: Basic variant-annotation-example-1

Variant occurrence ID relationship: Basic Single nucleotide variant

Annotation database: ClinVar

Variant origin: germline

Variant pathogenicity: pathogenic

Variant class level: ACMG Class 5

Variant tier level: Tier 1

Allele frequency: 0.0001

Medication: PARP inhibitor

identifier: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/NamingSystem/variant-annotation-id/VA0001

code: Clinical variant annotation

Source1

{
  "resourceType": "Basic",
  "id": "variant-annotation-example-1",
  "meta": {
    "profile": [
      "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/variant-annotation"
    ]
  },
  "text": {
    "status": "extensions",
    "div": "<!-- snip (see above) -->"
  },
  "extension": [
    {
      "url": "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/variant-annotation-variant-occurrence-ref",
      "valueReference": {
        "reference": "Basic/variant-occurrence-example-1"
      }
    },
    {
      "url": "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/variant-annotation-annotation-database",
      "valueString": "ClinVar"
    },
    {
      "url": "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/variant-annotation-variant-origin",
      "valueString": "germline"
    },
    {
      "url": "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/variant-annotation-variant-pathogeny",
      "valueString": "pathogenic"
    },
    {
      "url": "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/variant-annotation-variant-class-level",
      "valueString": "ACMG Class 5"
    },
    {
      "url": "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/variant-annotation-variant-tier-level",
      "valueString": "Tier 1"
    },
    {
      "url": "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/variant-annotation-allele-frequency",
      "valueDecimal": 0.0001
    },
    {
      "url": "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/variant-annotation-medication",
      "valueString": "PARP inhibitor"
    }
  ],
  "identifier": [
    {
      "system": "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/NamingSystem/variant-annotation-id",
      "value": "VA0001"
    }
  ],
  "code": {
    "coding": [
      {
        "system": "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/CodeSystem/variant-annotation-type",
        "code": "clinical",
        "display": "Clinical variant annotation"
      }
    ]
  }
}