Variant View

How is HGVS calculated in CVA Portal?

HGVS annotation in CVA Portal is obtained from CellBase which provides HGVS according to the recommendations here: https://varnomen.hgvs.org/recommendations/general/

How are transcripts selected HGVS annotation?

HGVS on the variant view page in CVA Portal can be seen for all transcripts by clicking on the side bar icon. On the main variant view page, the default HGVS transcript is selected based on the following rules:

1. The transcript must be "protein coding" - if more than one transcript satisfies this rule then...
2. The transcript must have an Ensembl "gencode basic" annotation flag - if more than one transcript satisfies this rule then...
3. The transcript with an "CCDS" annotation flag - if more than one transcript satisfies this rule then...
4. The transcript with the longest coding sequence length - if more than one transcript satisfies this rule then...
5. The transcript with the largest number of exons is selected

If there is still more than one transcript for a gene then one is selected at random

How do I find a list of all variants classed as Pathogenic or Likely Pathogenic?

This is currently not possible in the CVA Portal. It is a feature we wish to add ASAP.

How do I see a list of all Tier 1 variants?

This is currently not possible in the CVA Portal. It is a feature we wish to add ASAP.