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: iGene Variant Category

Active as of 2026-09-02

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<CodeSystem xmlns="http://hl7.org/fhir">
  <id value="IGeneVariantCategory"/>
  <language value="en"/>
  <text>
    <status value="generated"/>
    <div xmlns="http://www.w3.org/1999/xhtml"><p class="res-header-id"><b>Generated Narrative: CodeSystem IGeneVariantCategory</b></p><a name="IGeneVariantCategory"> </a><a name="hcIGeneVariantCategory"> </a><p>This case-sensitive code system <code>https://fhir.nwgenomics.nhs.uk/CodeSystem/IGeneVariantCategory</code> 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">SEQV<a name="IGeneVariantCategory-SEQV"> </a></td><td>Sequence Variant</td><td>A small-scale change in the DNA sequence at a specific gene/transcript location - substitution, insertion, deletion or indel.</td></tr><tr><td style="white-space:nowrap">ICNV<a name="IGeneVariantCategory-ICNV"> </a></td><td>Intragenic Copy Number Variant</td><td>A copy-number change (gain or loss) contained within a single gene, e.g. loss of one or more exons.</td></tr><tr><td style="white-space:nowrap">MCNV<a name="IGeneVariantCategory-MCNV"> </a></td><td>Multigenic Copy Number Variant</td><td>A copy-number change spanning a larger region covering multiple genes or a chromosome band.</td></tr><tr><td style="white-space:nowrap">SV<a name="IGeneVariantCategory-SV"> </a></td><td>Structural Variant</td><td>A large-scale rearrangement (translocation, inversion, complex event) that is not necessarily a simple copy-number gain or loss.</td></tr><tr><td style="white-space:nowrap">LOH<a name="IGeneVariantCategory-LOH"> </a></td><td>Loss of Heterozygosity</td><td>One parental copy of a region is lost or indistinguishable from the other - modelled as a separate Molecular Consequence Observation, not on Variant itself (see MolecularConsequence.fsh).</td></tr></table></div>
  </text>
  <url
       value="https://fhir.nwgenomics.nhs.uk/CodeSystem/IGeneVariantCategory"/>
  <version value="2.2.0"/>
  <name value="IGeneVariantCategory"/>
  <title value="iGene Variant Category"/>
  <status value="active"/>
  <experimental value="false"/>
  <date value="2026-09-02"/>
  <publisher value="NHS North West Genomics"/>
  <contact>
    <telecom>
      <system value="url"/>
      <value value="https://www.nwgenomics.nhs.uk/contact-us"/>
    </telecom>
  </contact>
  <description
               value="iGene's five variant-type categories, each with its own repeating set of custom
fields in iGene's &quot;Variant Level Data&quot; spec (`SEQV1`-`SEQV10`, `ICNV1`-`ICNV3`,
`MCNV1`-`MCNV3`, `SV1`-`SV3`, `LOH1`-`LOH2`) - see [OMICS DSS Result
Integration](reportable-variants.html#outstanding-issues) for the decision this
codifies: making &quot;which iGene slot type is this&quot; an explicit, coded
`Variant.component:variant-category` value instead of an inferred classification.

This extends LRI's own &quot;Variant category&quot; (LOINC `83005-9`), whose answer list
(`LL4165-8`) only distinguishes Simple Variant vs Structural Variant - not granular
enough to route a reported variant to the correct iGene slot type."/>
  <jurisdiction>
    <coding>
      <system value="urn:iso:std:iso:3166"/>
      <code value="GB"/>
      <display value="United Kingdom of Great Britain and Northern Ireland"/>
    </coding>
  </jurisdiction>
  <caseSensitive value="true"/>
  <content value="complete"/>
  <count value="5"/>
  <concept>
    <code value="SEQV"/>
    <display value="Sequence Variant"/>
    <definition
                value="A small-scale change in the DNA sequence at a specific gene/transcript location - substitution, insertion, deletion or indel."/>
  </concept>
  <concept>
    <code value="ICNV"/>
    <display value="Intragenic Copy Number Variant"/>
    <definition
                value="A copy-number change (gain or loss) contained within a single gene, e.g. loss of one or more exons."/>
  </concept>
  <concept>
    <code value="MCNV"/>
    <display value="Multigenic Copy Number Variant"/>
    <definition
                value="A copy-number change spanning a larger region covering multiple genes or a chromosome band."/>
  </concept>
  <concept>
    <code value="SV"/>
    <display value="Structural Variant"/>
    <definition
                value="A large-scale rearrangement (translocation, inversion, complex event) that is not necessarily a simple copy-number gain or loss."/>
  </concept>
  <concept>
    <code value="LOH"/>
    <display value="Loss of Heterozygosity"/>
    <definition
                value="One parental copy of a region is lost or indistinguishable from the other - modelled as a separate Molecular Consequence Observation, not on Variant itself (see MolecularConsequence.fsh)."/>
  </concept>
</CodeSystem>