Genomics Reporting Implementation Guide
2.0.0 - trial-use

This page is part of the Genetic Reporting Implementation Guide (v2.0.0: STU 2) based on FHIR R4. This is the current published version. For a full list of available versions, see the Directory of published versions

: Variant Confidence Status Codes - JSON Representation

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{
  "resourceType" : "CodeSystem",
  "id" : "variant-confidence-status-cs",
  "text" : {
    "status" : "generated",
    "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p>This code system http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/variant-confidence-status-cs defines the following codes:</p><table class=\"codes\"><tr><td style=\"white-space:nowrap\"><b>Code</b></td><td><b>Display</b></td><td><b>Definition</b></td></tr><tr><td style=\"white-space:nowrap\">high<a name=\"variant-confidence-status-cs-high\"> </a></td><td>High</td><td>High confidence true positive variant call. Suitable for clinical reporting.</td></tr><tr><td style=\"white-space:nowrap\">intermediate<a name=\"variant-confidence-status-cs-intermediate\"> </a></td><td>Intermediate</td><td>Candidate true positive variant call. Unable to confirm without additional testing.</td></tr><tr><td style=\"white-space:nowrap\">low<a name=\"variant-confidence-status-cs-low\"> </a></td><td>Low</td><td>High confidence false positive variant call.</td></tr></table></div>"
  },
  "url" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/variant-confidence-status-cs",
  "version" : "2.0.0",
  "name" : "VariantConfidenceStatusCS",
  "title" : "Variant Confidence Status Codes",
  "status" : "active",
  "date" : "2022-05-09T16:59:16+00:00",
  "publisher" : "HL7 Clinical Genomics Working Group",
  "contact" : [
    {
      "name" : "HL7 Clinical Genomics Working Group",
      "telecom" : [
        {
          "system" : "url",
          "value" : "http://www.hl7.org/Special/committees/clingenomics"
        },
        {
          "system" : "email",
          "value" : "cg@lists.HL7.org"
        }
      ]
    }
  ],
  "description" : "A code that represents the confidence of a true positive variant call.",
  "jurisdiction" : [
    {
      "coding" : [
        {
          "system" : "http://unstats.un.org/unsd/methods/m49/m49.htm",
          "code" : "001",
          "display" : "World"
        }
      ]
    }
  ],
  "caseSensitive" : true,
  "content" : "complete",
  "count" : 3,
  "concept" : [
    {
      "code" : "high",
      "display" : "High",
      "definition" : "High confidence true positive variant call. Suitable for clinical reporting."
    },
    {
      "code" : "intermediate",
      "display" : "Intermediate",
      "definition" : "Candidate true positive variant call. Unable to confirm without additional testing."
    },
    {
      "code" : "low",
      "display" : "Low",
      "definition" : "High confidence false positive variant call."
    }
  ]
}