ACVI-Med, an open source variant interpretation tool for medical genomics

BACKGROUND: The adoption of whole genome and exome sequencing (WGS/WES) is expanding rapidly, yet variant interpretation remains a critical bottleneck, limiting diagnostic yield and delaying precision care. We present ACVI-Med (Accelerated Candidate Variant Interpretation in Medicine), an open-source, on-premise platform for comprehensive analysis of genomic data. RESULTS: ACVI-Med integrates phenotype-aware filtering, ACMG-guided variant classification, and secondary findings detection into a unified, containerized system built for reproducibility and deployment across diverse institutional environments. Designed for accessibility, ACVI-Med enables users without extensive bioinformatics expertise to interpret variants from VCF (Variant Call Format) files through a flexible interface supporting phenotype-driven filtering, ACMG-guided variant classification, and integration of population, clinical, and predictive annotations. The software incorporates modules for secondary findings detection, aligned with ACMG Secondary Findings v3.2 recommendations, extending its utility beyond primary variant analysis. ACVI-Med’s customizable filtering logic, real-time access to curated knowledge bases, and interactive visualization tools support transparent and reproducible genomic interpretation. CONCLUSION: ACVI-Med is an open-source software for genomic variant interpretation. Unlike commercial solutions, ACVI-Med is cost-effective, containerized, and can be institutionally self-hosted, reducing barriers to adoption in research settings.