Introduction to VarSome's Germline and Somatic Variant Classification

VarSome provides access to over 140 public genomics-related databases through its purpose-built data storage system called MolecularDB (see VarSome’s Big Data). As data quality is of paramount importance to us, MolecularDB runs daily comprehensive data integrity checks and ensures genomics data are meticulously integrated and cross-referenced, and insertions and deletions are matched consistently across all the data resources available on VarSome. Besides that, you can rest assured there are always up-to-date data on VarSome. However, that’s not all.

In particular, VarSome is also a thriving global Human Genomics Community of healthcare professionals and researchers sharing knowledge in the form of variant classifications, publication links, or discussions. VarSome users can exchange research notes or even ask to be introduced to other users who wish to engage in a deeper collaboration.

One of the benefits of such a massive aggregated, harmonized and enriched database is that it can be applied in further downstream processes, such as automated variant classification according to the guidelines of the American College of Medical Genetics and Genomics (ACMG), or those developed by the Association for Molecular Pathology (AMP) for interpretation of somatic variants.

In 2015, ACMG and AMP published updated standards and guidelines for the clinical interpretation of sequence variants with respect to human diseases on the basis of 28 criteria [1]. This was followed, in 2017, by a joint recommendation by AMP, American Society of Clinical Oncology, and College of American Pathologists on standards and guidelines for the interpretation and reporting of sequence variants in cancer [2]. However, variability between individual interpreters can be extensive because of reasons such as the different understandings of these guidelines and the lack of standard algorithms for implementing them. To address these problems, VarSome has implemented 21 ACMG criteria for automated interpretation of the clinical significance of sequence variants with a manual adjustment step, as well as a robust evidence based logic to apply the AMP guidelines for the interpretation of cancer sequence variants.

To this extent, the main aim of VarSome’s ACMG and AMP implementations is to correctly present the most salient data available and help the users to quickly identify those variants that require additional clinical scrutiny.  For further information, you can visit  VarSome’s Implementation of ACMG Guidelines and VarSome's Implementation of AMP Guidelines.

Further suggested reading: