NHS North West Genomics
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CodeSystem: iGene Variant Category

Official URL: https://fhir.nwgenomics.nhs.uk/CodeSystem/IGeneVariantCategory Version: 2.2.0
Active as of 2026-09-02 Computable Name: IGeneVariantCategory

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 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.

This Code system is referenced in the definition of the following value sets:

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

CodeDisplayDefinition
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).

Description of the above table(s).