InterVar

Automated ACMG/AMP variant interpretation tool. Applies the 28 ACMG criteria systematically based on available evidence.

What It Does

• Automated application of ACMG/AMP criteria (PVS1, PS1-4, PM1-6, PP1-5, BA1, BS1-4, BP1-7)
• Uses: population frequency, computational predictions, functional data, clinical data
• Outputs evidence code assignments and final classification
• Command-line and web interface

How to Use

Web

1. Go to https://wintervar.wglab.org/
2. Enter variant in HGVS format
3. Review applied ACMG criteria

Command Line

# Install
git clone https://github.com/WGLab/InterVar.git
cd InterVar
 
# Run
python InterVar.py -i input.vcf -d humandb/ --buildver hg38

Verified Status

VERIFIED — wInterVar web API returns 404 for E1659A (variant not in their pre-computed database). Would need to run local InterVar installation with VCF input. Our manual ACMG (PM3_M + PP3_M + PM2_S = VUS) is already well-supported. InterVar unlikely to add new evidence since it uses the same predictors.

STRC Research Usage

• Compare automated ACMG classification vs our manual classification
• Useful as a “second opinion” on criteria application

Connections

• VarSome [see-also] — also does automated ACMG
• Franklin [see-also] — AI-powered classification
• STRC E1659A Conservation and Reclassification [see-also]