Variants Overview

CIViC variants are usually genomic alterations, including single nucleotide variants (SNVs), insertion/deletion events (indels), copy number alterations (CNV’s such as amplification or deletion), structural variants (SVs such as translocations and inversions), and other events that differ from the “normal” genome. In some cases a CIViC variant may represent events of the transcriptome or proteome. For example, ‘expression’ or ‘over-expression’ is a valid variant. Regardless of the variant, it must have an Predictive, Prognostic, Predisposing or Diagnostic clinical relevance to be entered in CIViC. New curators should generally avoid proposing new variants that are unlike any already in CIViC.

Variant Attributes

Attribute

Description

Source

Name

Description of the type of variant (e.g., ‘V600E’, ‘BCR-ABL fusion’, ‘Loss-of-function’, ‘Exon 12 mutations’). Should be as specific and short as possible (i.e., specific amino acid changes).

CIViC

Summary

User-defined summary of the clinical relevance of this Variant.

CIViC

Alias

Alternative names for this Variant. May be more verbose (e.g., ‘Val600Glu’) versions, dbSNP IDs or alternative nomenclature used in the literature.

CIViC

HGVS Expression

User-defined HGVS strings following HGVS nomenclature that represent this Variant at the DNA, RNA or protein level.

CIViC

ClinVar ID

User-defined ClinVar ID referencing this Variant which will be linked directly to ClinVar. A value of “None Specified” indicates that the variant has not been evaluated for a ClinVar ID. A value of “None Found” indicates that an attempt was made to find a matching ClinVar Entry, but none exists. A value of “N/A” indicates that a ClinVar record is not applicable to the variant (e.g. “Overexpression” variants).

CIViC (ClinVar)

Sources

A list of PubMed IDs referring to evidence supporting statements made in the Gene’s description. Source descriptions (e.g. ‘Weisberg et al., 2007, Nat. Rev. Cancer’) are pulled from the PubMed database at the time of submission, and are not editable.

CIViC (PubMed)

CIViC Actionability Score

The CIViC Actionability Score assesses the quality and quantity of evidence submitted for each variant. The CIViC Actionability Score is calculated by adding all Evidence Item Scores for each variant. The Evidence Item Score is calculated by multiplying the evidence level (A=10 points, B=5 points, C=3 points, D=1 point, E=0.25 points) by the evidence rating (Each Star = 1 point).

CIViC

Variant Type(s)

One or more terms from the Sequence Ontology that describes the type of variant. Should be the most descriptive term applicable on a given branch (e.g., ‘Conservative Missense Variant’, ‘Stop Gained’, ‘Transcript Fusion’).

CIViC (Sequence Ontology)

Primary Coordinates

Reference Build

NCBI or GRC human reference assembly version.

CIViC

Chromosome

Name of the chromosome in which the variant occurs.

CIViC

Start, Stop

Start and stop positions of the variant (1-based genome coordinate). Start must be less than or equal to stop.

CIViC

Reference & Variant Bases

The nucleotide base of the reference and variant allele (e.g. ‘C’, ‘A’).

CIViC

Representative Transcript

Ensembl transcript ID and version number for a known transcript of the gene that contains the variant (e.g. ‘ENST00000263967.3’).

CIViC

Secondary Coordinates

Same as Primary

For fusion variants, the secondary coordinates are used to specify the 3’ partner of the fusion gene.

CIViC

MyVariant.Info

MyVariant Info

Data retrieved from MyVariant.Info using the curated Primary Coordinates (chromosome, start, stop, reference base, variant base) described above as the query. Includes external IDs and links whenever possible with additional data displayed by clicking the “Details” button.

MyVariant.Info