Name

The Variant Name describes the specific variant being interpreted for clinical utility. Clicking on a variant name in the variant list for a gene will bring up a variant specific page with description, coordinates, alises, and associated Evidence Items.

Understanding Variant Names

The variant name describes concisely some defining feature of the variant for rapid and clear identification. This will often follow HGVS-style conventions (e.g. L858R) and can also be highly generalized to categorical type (also called “bucket” type) variants such as MUTATION (for EGFR), or EXON 11 MUTATION (for KIT), which often arise during studies that pool larger numbers of patients with mutation in the given gene or gene region, in order to reach statistical conclusions. The variant name will reflect the specific biological alteration whenever possible (e.g. T790M) and also, whenever it is defined, refer to the underlying changes to the DNA sequence.

New CIViC Variants are entered into the database during the first instance of curation of evidence for the given variant. At the time of entering an Evidence Item for the new variant, the user generates the name by entering it into the Variant Name field, below the Gene Entrez Name field. Unlike Entrez name, which is drawn from a list of predetermined gene names, the variant is free text for the curator.

Screenshot of Gene and Variant fields in the Add Evidence form

Figure 1: Screenshot of Gene and Variant fields in the Add Evidence form

Curating Variant Names

When curating this field, the most specific Variant Name described by the source should be used (e.g. KRAS G12/G13 rather than KRAS Exon 2 Mutation). The Variant Name can be very specific [e.g. VHL R176fs (c.528delG)], and in these cases HGVSor can refer to a collection of variants fitting a named category (i.e. categorical variants, sometimes called bucket variants). Examples of categorical variants include KRAS G12/G13, EGFR Exon 20 Insertion, and PIK3CA Mutation. Categorical variants are associated with multiple ClinVar entries, if applicable. Other Variant Names, including star-allele nomenclature adopted by pharmacogenetics field (e.g. DPYD*2A) are also supported.

Variant name

Gene

Variant type (Sequence Ontology)

Demonstrates support of…

DPYD*2A Homozygosity

DPYD

Splice Donor Variant

pharmacogenomic nomenclature

ALK Fusions

ALK

Transcript Fusion

fusions with an unknown partner common in FISH techniques

EML4-ALK

ALK

Transcript Fusion

specific gene fusions

EML4-ALK E6;A20

ALK

Transcript Fusion

fusions with known specific exon boundaries / specific fusion isoforms

BCR-ABL T315I

ABL1

Missense Variant

specific variants in the context of other variants

CDKN2A Promoter Hypermethylation

CDKN2A

N/A

epigenetic modifications

p16 Expression

CDKN2A

N/A

expression changes

rs3814960

CDKN2A

5 Prime UTR Exon Variant

polymorphisms

FLT3-ITD

FLT3

Inframe Insertion

imprecise insertions with shared consequences

Exon 11 Mutation

KIT

Coding Sequence Variant

categorical variants covering specific transcriptional boundaries

DNA Binding Domain Mutation

TP53

DNA Binding Site

categorical variants covering specific functional boundaries

Exon 14 Skipping Mutation

MET

Exon Loss Variant

categorical variants covering specific transcriptional consequences

Loss-of-function

BRCA

Loss of Function Variant

categorical variants covering specific functional consequences