Variant Details

This page shows the annotation and other information about a variant.

The top of the page has an IGV link, and a link to the allele for this variant: ../_images/variant_details_top.png

An allele is genome build independent - ie hg19 and hg38 variants for same change point to same allele. The ID (CA9034) is from the ClinGen Allele Registry

Classifications

../_images/variant_details_classifications.png Variant Details - Classification section

This shows internal classifications for an allele (may have been classified against a different genome build)

The far right column contains Classification Flags

Transcripts

Variant annotation is calculated for each transcripts overlapping a variant. You can select each of the different transcripts to change which is being displayed. A transcript can be labelled as Representative (most damaging for variant shown on analysis grid) or canonical (transcript chosen for gene by RefSeq/Ensembl)

Samples

At the bottom of the page is a grid of samples that contain the variant (and the zygosity and read information). Only samples you have permissions to view are shown, but a warning will be shown informing you that samples you don’t have permission to see exist.