VarSome & VarSome Clinical v.9.5.0

VarSome 9.5 introduces a series of improvements to the frontend, designed to improve usability and make it easier to help you find the information you're looking for. We've also updated our ACMG and AMP Classifiers. Thank you as always for the continued feedback and support - it is tremendously helpful!

VarSome 9.5

Classifiers

ACMG - Germline

BP3 & PP4: For VarSome Premium and Clinical users, CADD will now replace DANN, instead of evaluating both.

BP1 & PP2: Based on user feedback, we have reverted to our previous implementation using statistics derived from clinically reported variants, instead of using the GnomAD Z-Score for the gene.

AMP - Somatic

The “Pathway” rule now presents more descriptive explanations from JAX CKB and KEGG of why a given gene relates to cancer. note: JAX CKB is only licensed for VarSome Clinical

VarSome

Databases

VarSome now integrates well over 100 sources of data! In order to help stay on top of this we have created a new page that lists all VarSome data sources and versions.

Clicking on the individual database name will take you to the website for that data source, if available.

Performance

We have significantly improved the performance of the VarSome front-end, particularly when viewing a variant or gene with a large number of publications:

Usability

We’ve also improved the legibility and position of pop-ups to ensure the relevant data is easier to read:

We have added linked publications to our UniProt Variants component and ensured the reported pathogenicity is highlighted:

If a transcript version is not found we have now added a more informative error message.

VarSome Clinical

AMP & JAX CKB

JAX CKB is now enabled by default in all tumour samples. Please contact us if you want to disable JAX for your group or organization.

You can confirm this group setting at the top of the launch analysis screen:

Having JAX CKB enabled may improve your classification result. 

And provides additional information about your samples. 

Improved Coverage Reports

We have amended the coverage categories for germline variant detection for regions with a coverage of >20x to make the coverage report more meaningful.  

Before :

After :

Further Information and Support

Not already a VarSome Premium or VarSome Clinical user? Get in touch and ask for a free trial.

As ever we hope you find these changes and improvements helpful, we’d love to hear any suggestions you may have, support is available as usual from support@varsome.com

- The VarSome Team