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 in its permanent home (it will always be available at this URL). For a full list of available versions, see the Directory of published versions

: Variant Confidence Status Codes - XML Representation

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<CodeSystem xmlns="http://hl7.org/fhir">
  <id value="variant-confidence-status-cs"/>
  <text>
    <status value="generated"/>
    <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>
  </text>
  <url
       value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/variant-confidence-status-cs"/>
  <version value="2.0.0"/>
  <name value="VariantConfidenceStatusCS"/>
  <title value="Variant Confidence Status Codes"/>
  <status value="active"/>
  <date value="2022-05-09T16:53:07+00:00"/>
  <publisher value="HL7 Clinical Genomics Working Group"/>
  <contact>
    <name value="HL7 Clinical Genomics Working Group"/>
    <telecom>
      <system value="url"/>
      <value value="http://www.hl7.org/Special/committees/clingenomics"/>
    </telecom>
    <telecom>
      <system value="email"/>
      <value value="cg@lists.HL7.org"/>
    </telecom>
  </contact>
  <description
               value="A code that represents the confidence of a true positive variant call."/>
  <jurisdiction>
    <coding>
      <system value="http://unstats.un.org/unsd/methods/m49/m49.htm"/>
      <code value="001"/>
      <display value="World"/>
    </coding>
  </jurisdiction>
  <caseSensitive value="true"/>
  <content value="complete"/>
  <count value="3"/>
  <concept>
    <code value="high"/>
    <display value="High"/>
    <definition
                value="High confidence true positive variant call. Suitable for clinical reporting."/>
  </concept>
  <concept>
    <code value="intermediate"/>
    <display value="Intermediate"/>
    <definition
                value="Candidate true positive variant call. Unable to confirm without additional testing."/>
  </concept>
  <concept>
    <code value="low"/>
    <display value="Low"/>
    <definition value="High confidence false positive variant call."/>
  </concept>
</CodeSystem>