PROTECT-CHILD Pediatric Transplant Data Implementation Guide, published by Protect Child. This guide is not an authorized publication; it is the continuous build for version 0.1.0-ci-build built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/hl7-eu/protect-child/ and changes regularly. See the Directory of published versions

• Narrative Content
• XML
• JSON
• TTL

: Example Variant Occurrence - JSON Representation

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{
  "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" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p class=\"res-header-id\"><b>Generated Narrative: Basic variant-occurrence-example-1</b></p><a name=\"variant-occurrence-example-1\"> </a><a name=\"hcvariant-occurrence-example-1\"> </a><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\"/><p style=\"margin-bottom: 0px\">Profile: <a href=\"StructureDefinition-variant-occurrence.html\">Variant Occurrence</a></p></div><p><b>Target region ID relationship</b>: <a href=\"Basic-target-region-example-1.html\">Basic Gene-level target region</a></p><p><b>Reference sequence</b>: NM_007294.4</p><p><b>dbSNP rsID</b>: rs80357713</p><p><b>Reference allele</b>: A</p><p><b>Alternate allele</b>: C</p><p><b>HGVS c. notation</b>: c.5266dupC</p><p><b>HGVS p. notation</b>: p.(Gln1756Profs*74)</p><p><b>Variant read depth</b>: 120</p><p><b>Variant exon number</b>: 20</p><p><b>Copy number</b>: 2</p><p><b>CNV locus</b>: chr17:43044295-43125482</p><p><b>Fusion breakpoint</b>: NA</p><p><b>Fusion supporting reads</b>: 0</p><p><b>Sequence alteration</b>: missense_variant</p><p><b>Variant feature</b>: pathogenic_variant</p><p><b>Genetic origin</b>: somatic</p><p><b>Genotype</b>: heterozygous</p><p><b>identifier</b>: <code>https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/NamingSystem/variant-occurrence-id</code>/VO0001</p><p><b>code</b>: <span title=\"Codes:{https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/CodeSystem/variant-occurrence-type snv}\">Single nucleotide variant</span></p></div>"
  },
  "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"
      }
    ]
  }
}