Welcome to VIP-HL

Variant Interpretation Platform for Genetic Hearing Loss

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Example: GJB2, 13-20763044-A-C, rs111033313, GJB2 c.250G>A, SLC26A4 p.Glu29Gly, NM_004004.5:c.109G>A, NP_000432.1:p.Lys52Ter

The American College of Medical Genetics and Genomics, and the Association for Molecular Pathology (ACMG/AMP) have proposed a set of evidence‐based guidelines to support sequence variant interpretation. The ClinGen hearing loss expert panel (HL‐EP) introduced further specifications into the ACMG/AMP framework for genetic hearing loss (Oza et al. 2018).

We developed a tool named Variant Interpretation Platform for genetic Hearing Loss (VIP-HL), aiming to semi‐automate the HL ACMG/ AMP rules. VIP‐HL aggregates information from external databases to automate 13 out of 24 ACMG/AMP rules specified by HL‐EP, namely PVS1, PS1, PM1, PM2, PM4, PM5, PP3, BA1, BS1, BS2, BP3, BP4, and BP7 (Xiang et al. 2020; Peng et al. 2021). We benchmarked VIP‐HL using 50 variants in which 82 rules were activated by the ClinGen HL‐EP. VIP‐HL is an integrated online tool for reliable automated variant classification in hearing loss genes. It assists curators in variant interpretation and provides a platform for users to share classifications with each other.

Getting more information from the VIP-HL paper.

Reference: Xiang J, Peng J, Baxter S, Peng Z. AutoPVS1: An automatic classification tool for PVS1 interpretation of null variants. Hum Mutat. 2020;41(9):1488-1498. (Editor's choice and cover article) Peng J, Xiang J, Jin X, et al. VIP-HL: Semi-automated ACMG/AMP variant interpretation platform for genetic hearing loss. Hum Mutat. 2021;42(12):1567-1575. (Cover article) Oza AM, DiStefano MT, Hemphill SE, et al. Expert specification of the ACMG/AMP variant interpretation guidelines for genetic hearing loss. Hum Mutat. 2018;39(11):1593-1613.

ClinGen:   https://search.clinicalgenome.org/kb/gene-validity