Platform Updates VarSome Clinical ACMG Release

VarSome Clinical 11.4

By Richard Meyer on November, 3 2022

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Richard Meyer


Key New Features

  • ACMG classification updated to use the points-based verdict per ClinGen guidelines
  • Sample Information now includes Runs of Homozygosity metrics
  • Additional CNV caller for WGS samples
  • New ClinGen database
  • OMIM filter to remove non-associated phenotypes
  • New filter by number of matched phenotypes
  • Improved filter for top VUS variants

New Features

New ClinGen Variants Database integrated in VarSome and VarSome Clinical

A new card containing curated data from ClinGen variants database is now available in VarSome and VarSome Clinical.

This information will be available when the queried variant has already been curated by any of the ClinGen expert panels. It will display crucial information such as curated pathogenicity, associated phenotypes, and comments submitted by curators.

Sample and Analysis Information - Runs of Homozygosity (ROH)

Analyses are now scanned for the presence of extended regions of homozygosity. Summary ROH data are displayed in Sample/Analysis Information, including percentage of autozygosity FROH, which is computed for several length thresholds.

Additional CNV caller for WGS samples

An additional solution for CNV calling is available for WGS sample cohorts. The tried-and-tested read-depth method, which is already in use for WES and panel samples, offers improved recall of long CNVs complemented by concise and intuitive visualizations. The standard Delly-based solution remains available for single WGS samples.

To use this approach, select multiple WGS samples on the CNV launch analysis page and launch the analysis using them.


ACMG Classification

Important: please see the VarSome 11.4 release note for the full list of ACMG changes that are now fully integrated into VarSome Clinical.

  • The ACMG classification has been updated to use the points-based verdict recommended in the latest ClinGen guidelines
  • Rule PM2 now always has strength "supporting"
  • The new guidelines for calibrated in-silico predictions have been implemented
  • The classifier will give precedence to MANE transcripts when available
  • In addition: the strength of in-silico predictions are reduced if there is significant clinical evidence to the contrary

Deleting Samples

On the Sample page we have now added 3 new options for deleting samples:

  • Archive sample data
  • Delete FASTQ sample data
  • Delete BAM sample data

Multi Sample Analysis

We have provided the option to run Multi-Sample analysis for somatic samples from a VCF. 

For example, any trio analysis samples you have will now appear in the launch screen as an option for selection.


OMIM Phenotypes Filter

A new dynamic filter option has been added that provides the option to keep or filter out variants where their related gene has no associated OMIM phenotype 

Phenotypes Filter

Currently we only report on a sample’s phenotypes that are associated with a variant’s gene. This is displayed in the Phenotype column.  We have now provided the option to filter variants linked to a given number of matched phenotypes. 

Pathogenicity Class filter

Additional VUS categories have been added to the pathogenicity class dynamic filter.

Gene List Selection Filter

The Gene list search has been simplified so it is easier to make a search through the gene list filters.

New Assay Request Form

It is now possible to complete a standard online form to request the creation of a new assay.

The submitted form will be reviewed by our support team.

  • Select “New Assay Request” from the “Support & Manual” option at the top menu


  • Select “Your assay is not in the list” in the “Launch Analysis” screen.


VarSome Clinical Dashboard

We have added to the dashboard the 'Total' and 'Monthly' number of samples analyzed. 

Changes in CNV FASTQ analysis

Re-Enabled WGS tumor-normal CNV analysis 

The option to analyze WGS tumor/normal CNVs has been reintroduced.  To run this option, on the CNV launch analysis page select both, one tumor normal and one normal sample and launch the analysis using them both. 

AMP Classification

JAX CKB Improvements

JAX CKB have recently announced several new features that we have been quick to incorporate - this is a licensed database and only available to users for VarSome Clinical.

On the gene results page, within the JAX CKB information, a new table has been provided that presents all relevant clinical trials from Germany, Spain, Italy, France, Austria and Belgium but not the US or Canada. The clinical trials are all curated from The table can be searched using the title, phase, recruitment status or NCID code.

Improved base quality recalibration for amplicon kits

We have modified our amplicon analysis pipeline to use GATK recalibration tool (BaseRecalibrator)  to allow detection of variants that were previously missed because they failed to pass the  average base quality cutoff value.  In some cases, such variants will still be labeled as failed, in which case the users can find them by checking 'Variant list will contain all variants' while launching a new analysis.

Further Information and Support

Not already a 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


- The VarSome Team

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