NHS North West Genomics
2.2.0 - ci-build
NHS North West Genomics
2.2.0 - ci-build
NHS North West Genomics - Local Development build (v2.2.0) built by the FHIR (HL7® FHIR® Standard) Build Tools. See the Directory of published versions
| Active as of 2026-09-02 |
{
"resourceType" : "CodeSystem",
"id" : "IGeneVariantCategory",
"language" : "en",
"text" : {
"status" : "generated",
"div" : "<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>"
},
"url" : "https://fhir.nwgenomics.nhs.uk/CodeSystem/IGeneVariantCategory",
"version" : "2.2.0",
"name" : "IGeneVariantCategory",
"title" : "iGene Variant Category",
"status" : "active",
"experimental" : false,
"date" : "2026-09-02",
"publisher" : "NHS North West Genomics",
"contact" : [
{
"telecom" : [
{
"system" : "url",
"value" : "https://www.nwgenomics.nhs.uk/contact-us"
}
]
}
],
"description" : "iGene's five variant-type categories, each with its own repeating set of custom\nfields in iGene's \"Variant Level Data\" spec (`SEQV1`-`SEQV10`, `ICNV1`-`ICNV3`,\n`MCNV1`-`MCNV3`, `SV1`-`SV3`, `LOH1`-`LOH2`) - see [OMICS DSS Result\nIntegration](reportable-variants.html#outstanding-issues) for the decision this\ncodifies: making \"which iGene slot type is this\" an explicit, coded\n`Variant.component:variant-category` value instead of an inferred classification.\n\nThis extends LRI's own \"Variant category\" (LOINC `83005-9`), whose answer list\n(`LL4165-8`) only distinguishes Simple Variant vs Structural Variant - not granular\nenough to route a reported variant to the correct iGene slot type.",
"jurisdiction" : [
{
"coding" : [
{
"system" : "urn:iso:std:iso:3166",
"code" : "GB",
"display" : "United Kingdom of Great Britain and Northern Ireland"
}
]
}
],
"caseSensitive" : true,
"content" : "complete",
"count" : 5,
"concept" : [
{
"code" : "SEQV",
"display" : "Sequence Variant",
"definition" : "A small-scale change in the DNA sequence at a specific gene/transcript location - substitution, insertion, deletion or indel."
},
{
"code" : "ICNV",
"display" : "Intragenic Copy Number Variant",
"definition" : "A copy-number change (gain or loss) contained within a single gene, e.g. loss of one or more exons."
},
{
"code" : "MCNV",
"display" : "Multigenic Copy Number Variant",
"definition" : "A copy-number change spanning a larger region covering multiple genes or a chromosome band."
},
{
"code" : "SV",
"display" : "Structural Variant",
"definition" : "A large-scale rearrangement (translocation, inversion, complex event) that is not necessarily a simple copy-number gain or loss."
},
{
"code" : "LOH",
"display" : "Loss of Heterozygosity",
"definition" : "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)."
}
]
}