v1.1.145 Release Notes

01 August 2019

Summary

Clinical Variant Ark (CVA) Portal is the visual gateway into the knowledge base built from rare disease cases and variants within the Genomics England Interpretation Platform.

You can access CVA Portal, using your existing Genomics England username and password here, www.cva.genomicsengland.nhs.uk

These are updated release notes following a delay in the previous release and updated functionality being included.

In this release we have focused on adding some pathogenicity “tags” to the variants in CVA so users can quickly identify whether their variant has been previously interpreted by another laboratory. Additionally, it is now possible to filter variant search results by gene symbol and its consequence type

New features and improvements

  • Changed the ordering of the HPO term list on the variant page so that the mostly frequent HPO terms are displayed first. Previously they were alphabetical (CZFE-503)
  • Case search results can now be filtered by clinical indication (CZFE-610)
  • Added filters on the variant search results for gene HGNC symbol and variant consequence type (CZFE-584)

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  • Examples in the “Search” drop down menu are now “clickable” (CZFE-231)
  • Overlapping genes on the variant page are now represented as “tiles” and include the most severe consequence type (CZFE-448)
  • Provided a warning message to users when a region search is performed that is greater than the current 1Mb maximum limit (CZFE-507)
  • Added to the variant search results a summary of the ACMG classifications for that variant and highlight if there are any conflicts (CZFE-537)

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  • Added the pathogenicity tag to the variant page (CZFE-536)

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  • The list of cases on the variant view has been paginated so it now loads in blocks of 20 at a time (CZFE-556)
  • The page loading icon updated
  • Completed internal testing of the gms-beta instance of CVA so it is ready for NGIS BETA using AD credentials https://cva-gms-beta.genomicsengland.nhs.uk

Fixed

  • Bug associated with clearing some of the case and variant filters (CZFE-591)

Known issues

  • It is not currently possible to filter variant search results by pathogenicity, we are working on this for future releases
  • Some pages are taking a while to load (>15 secs), we are looking into performance enhancements

Access

  • CVA Portal BETA can be accessed on the HSCN network here cva.genomicsengland.nhs.uk

Providing feedback

We have been developing the CVA Portal with input on requirements from a number of different users from GMCs and GeCIPs, if you would like to be involved please contact the Genomics England Service Desk .