Variant characterizations are viewable and queryable through a lightweight web application. Characterization is divided into multiple independent stages that each record zero or more annotations for each variant according to the type of characterization being performed by the stage.
At the end of characterization, variant annotations are aggregated and submitted to a variant classifier which assigns an American College of Medical Genetics (ACMG) category to each based on the accumulated annotation evidence, with the most damaging category achieved being the final categorization.
Characterization stages use a variety of software and data from both internal and external sources. The stages include:
ENSEMBL Variant Effect Predictor (VEP)
Comparison with dbSNP
CMH splice impact evaluator
CMH transcript context characterizer
Comparison with Human Gene Mutation Database (HGMD/GenomeTrax)