VarSeq 2.4.0 Has Been Released!

         May 24, 2023

Greetings VarSeq users! VarSeq 2.4.0 has officially been released. VarSeq 2.4.0 is a significant release that focuses on enhancing the VSClinical ACMG workflow by introducing new features and noteworthy improvements. The major highlights of the release are:

1. Welcoming structural variant support to the VSClinical ACMG workflow

  • Manually add or automatically bring SVs in from VarSeq projects to evaluations
  • New Assessment catalog to save SV interpretations and classifications
  • Updated report templates that support SVs

2. ACMG workflow automation has been enhanced via the application of evaluation scripts and through updates within VSPipeline to plug variants, CNVs, and SVs into a clinical report.

  • Import Project Variants, CNVs, and Fusions evaluation script
  • Sync Report Status with Variant Sets evaluation script
  • The Import Disease and Phenotype JSON evaluation script
  • The Remove Benign Variants evaluation script

3. The ACMG classification engines for variants and CNVs have been updated to handle certain edge case variants more accurately.

  • ACGS and ACMG classification updates affecting the application of PP3, PVS1, BP4, BP7, BS2, PS1, and PM5 criterion.
  • ACMG CNV classification updates for applying 2F, 2G, 2B, 2D and 2H criterion

If those features aren’t enough to get you excited about 2.4.0, allow me to focus on some other noteworthy features and improvements that might be more enticing.

For all the AMP users out there, you can look forward to improved clinical trial searching and generating tier II interpretations based on clinical trials. Within a few clicks, you can add biomarkers to an evaluation, utilize a new evaluation to add interpretations with tier II evidence, and report those biomarkers with interpretations and the relevant clinical trials!

Are you importing structural variants to VarSeq? The Match Gene List, Match Genes and Panels, and Match String List algorithms have now been made available for use to annotate break-end tables. In addition, the gene annotation algorithm will now predict the effect of a break-end that overlaps a UTR region.

There are many other hidden gem features and upgrades in this release, so I recommend checking out the VarSeq 2.4.0 release notes to see a complete list of new features along with identified bugs and their fixes. Please reach out to if you have questions about details regarding the release or need assistance upgrading to VarSeq 2.4.0!

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