FHIRsmith: CodeSystem/CodeSystem-IGeneVariantCategory.json

FHIR IG analytics

Package	fhir.nwgenomics.nhs.uk
Resource Type	CodeSystem
Id	CodeSystem-IGeneVariantCategory.json
FHIR Version	R4
Source	https://build.fhir.org/ig/nw-gmsa/nw-gmsa.github.com/CodeSystem-IGeneVariantCategory.html
URL	https://fhir.nwgenomics.nhs.uk/CodeSystem/IGeneVariantCategory
Version	2.2.0
Status	active
Date	2026-09-02
Name	IGeneVariantCategory
Title	iGene Variant Category
Realm	us
Authority	hl7
Description	iGene's five variant-type categories, each with its own repeating set of custom fields in iGene's "Variant Level Data" 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 "which iGene slot type is this" an explicit, coded `Variant.component:variant-category` value instead of an inferred classification. This extends LRI's own "Variant category" (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.
Content	complete

Resources that use this resource

ValueSet
fhir.nwgenomics.nhs.uk#current	IGeneVariantCategoryVS	iGene Variant Category

Resources that this resource uses

No resources found

Narrative

Note: links and images are rebased to the (stated) source

Generated Narrative: CodeSystem IGeneVariantCategory

This case-sensitive code system https://fhir.nwgenomics.nhs.uk/CodeSystem/IGeneVariantCategory defines the following codes:

Code	Display	Definition
SEQV	Sequence Variant	A small-scale change in the DNA sequence at a specific gene/transcript location - substitution, insertion, deletion or indel.
ICNV	Intragenic Copy Number Variant	A copy-number change (gain or loss) contained within a single gene, e.g. loss of one or more exons.
MCNV	Multigenic Copy Number Variant	A copy-number change spanning a larger region covering multiple genes or a chromosome band.
SV	Structural Variant	A large-scale rearrangement (translocation, inversion, complex event) that is not necessarily a simple copy-number gain or loss.
LOH	Loss of Heterozygosity	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).

Source1

{
  "resourceType": "CodeSystem",
  "id": "IGeneVariantCategory",
  "text": {
    "status": "generated",
    "div": "<!-- snip (see above) -->"
  },
  "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)."
    }
  ]
}