STP — Clinical Bioinformatics - Genomics

VASA: An ACMG Variant Scoring Assistant for Sequence Variant Classification, Variant Review and Teaching

Last updated: 10th September 2020


The ever-increasing volume and complexity of sequence variants requiring analysis in clinical labs prompted the American College of Medical Genetics and Genomics (ACMG) to revisit their variant interpretation guidelines in 2015. With the subsequent adoption of these guidelines in the UK, there is a need to ensure the technical and procedural workflows exist in the laboratory to meet these new standards. An agile project methodology was employed to develop a software solution to address this need. Based on the requirements of two clinical laboratories; the Molecular Pathology Laboratory at Kings College Hospital and the South West Thames Regional Genetics Service at St. Georges Hospital, this project describes a new application; the VAriant Scoring Assistant (VASA). VASA is a web-based tool developed in Django, that guides a user through the process of classifying variants against the ACMG guidelines, recording the associated evidence and calculating the pathogenicity score. An API has been created so it can be easily incorporated into existing variant interpretation workflows. A validation process was completed demonstrating that VASA is now ready to be used to support clinical laboratories in the classification and management of sequence variants.