ClassifyCNV: a tool for clinical annotation of copy-number variants

Abstract

SummaryCopy-number variants (CNVs) are an important part of human genetic variation. They can be benign or can play a role in human disease by creating dosage imbalances and disrupting genes and regulatory elements. Accurate identification and clinical annotation of CNVs is essential when evaluating patients with neurodevelopmental disorders and congenital anomalies. Here, we present ClassifyCNV, a tool that implements the 2019 ACMG classification guidelines to assess CNV pathogenicity. ClassifyCNV uses genomic coordinates and CNV type as input and reports the clinical classification for each variant along with a classification score breakdown and a list of genes that could be important for variant interpretation. The tool is suitable for integration into NGS analysis pipelines and facilitates high-throughput CNV analysis. Availability and implementationClassifyCNV is implemented in Python 3 and runs on UNIX, Linux and Mac OS X. The source code is available at https://github.com/Genotek/ClassifyCNV.