FHIRsmith: Basic/Basic-variant-occurrence-example-1.json

FHIR IG analytics

Package	pc.ig
Resource Type	Basic
Id	Basic-variant-occurrence-example-1.json
FHIR Version	R4

Resources that use this resource

No resources found

Resources that this resource uses

No resources found

Narrative

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

Generated Narrative: Basic variant-occurrence-example-1

Profile: Variant Occurrence

Target region ID relationship: Basic Gene-level target region

Reference sequence: NM_007294.4

dbSNP rsID: rs80357713

Reference allele: A

Alternate allele: C

HGVS c. notation: c.5266dupC

HGVS p. notation: p.(Gln1756Profs*74)

Variant read depth: 120

Variant exon number: 20

Copy number: 2

CNV locus: chr17:43044295-43125482

Fusion breakpoint: NA

Fusion supporting reads: 0

Sequence alteration: missense_variant

Variant feature: pathogenic_variant

Genetic origin: somatic

Genotype: heterozygous

identifier: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/NamingSystem/variant-occurrence-id/VO0001

code: Single nucleotide variant

Source1

{
  "resourceType": "Basic",
  "id": "variant-occurrence-example-1",
  "meta": {
    "profile": [
      "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/variant-occurrence"
    ]
  },
  "text": {
    "status": "extensions",
    "div": "<!-- snip (see above) -->"
  },
  "extension": [
    {
      "url": "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/variant-occurrence-target-region-ref",
      "valueReference": {
        "reference": "Basic/target-region-example-1"
      }
    },
    {
      "url": "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/variant-occurrence-reference-sequence",
      "valueString": "NM_007294.4"
    },
    {
      "url": "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/variant-occurrence-rs-id",
      "valueString": "rs80357713"
    },
    {
      "url": "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/variant-occurrence-reference-allele",
      "valueString": "A"
    },
    {
      "url": "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/variant-occurrence-alternate-allele",
      "valueString": "C"
    },
    {
      "url": "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/variant-occurrence-hgvs-c",
      "valueString": "c.5266dupC"
    },
    {
      "url": "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/variant-occurrence-hgvs-p",
      "valueString": "p.(Gln1756Profs*74)"
    },
    {
      "url": "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/variant-occurrence-variant-read-depth",
      "valueInteger": 120
    },
    {
      "url": "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/variant-occurrence-variant-exon-number",
      "valueInteger": 20
    },
    {
      "url": "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/variant-occurrence-copy-number",
      "valueDecimal": 2
    },
    {
      "url": "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/variant-occurrence-cnv-locus",
      "valueString": "chr17:43044295-43125482"
    },
    {
      "url": "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/variant-occurrence-fusion-breakpoint",
      "valueString": "NA"
    },
    {
      "url": "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/variant-occurrence-fusion-supporting-reads",
      "valueInteger": 0
    },
    {
      "url": "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/variant-occurrence-sequence-alteration",
      "valueString": "missense_variant"
    },
    {
      "url": "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/variant-occurrence-variant-feature",
      "valueString": "pathogenic_variant"
    },
    {
      "url": "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/variant-occurrence-genetic-origin",
      "valueString": "somatic"
    },
    {
      "url": "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/variant-occurrence-genotype",
      "valueString": "heterozygous"
    }
  ],
  "identifier": [
    {
      "system": "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/NamingSystem/variant-occurrence-id",
      "value": "VO0001"
    }
  ],
  "code": {
    "coding": [
      {
        "system": "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/CodeSystem/variant-occurrence-type",
        "code": "snv",
        "display": "Single nucleotide variant"
      }
    ]
  }
}