Genomic Prediction Tool

Single variant or batch VCF file prediction

Genome Version:

Select the reference genome version

Select Models to Run:

AlphaGenome HyenaDNA NT Model AlphaMissense ESM-1b GPN-MSA popEVE Evo2 (Local)

Chr:

Example: chr17, chr3, 1

Position:

Example: 7577121, 123456

Reference:

Example: A, G

Alternate:

Example: T, C

Variant (Chr-Pos-Ref-Alt):

Format: Chr-Position-Reference-Alternate (e.g., 1-66565-A-T or chr1-66565-A-T)

Genome Version:

Select the reference genome version for VCF file

Upload VCF File:

📁 Click or drag VCF file here

Supports .vcf and .vcf.gz format (Max 20MB)

Select Models to Run:

Include AlphaGenome Include HyenaDNA Include NT Model Include AlphaMissense Include ESM-1b Include GPN-MSA Include popEVE Include Evo2 (Local)

📧 Email Notification (Optional)

Batch prediction of large VCF files can take a long time. Enter your email and click Submit — we'll process your file on the server and send you an email when results are ready. You can safely close this page after submitting.

Leave blank to process immediately in your browser (you must keep this page open).

Prediction Results

Variant:

⚠️ Multiple Transcripts Detected:

🧬 MERGE Pathogenicity Prediction

Scores from all sub-models are assembled as features (multi-transcript values are averaged), missing values are imputed using MICE based on training distribution, then MinMax normalized. The final pathogenicity probability is computed by the MERGE model.

AlphaGenome Results

HyenaDNA Results

NT Model Results

AlphaMissense Results

ESM-1b Results

GPN-MSA Results

popEVE Results

Evo2 (Local) Results

Evo2 queries the local model with the upstream genomic context to obtain scores. LLR = Reference Score - Variant Score.

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Batch Prediction Results

Total Variants Processed

Total Transcripts Rendered

Variant (Chr:Pos Ref>Alt)	Transcript	Gene	🧬 MERGE Score	AlphaGenome	HyenaDNA	NT Score	AlphaMissense	ESM-1b	GPN-MSA	popEVE	Evo2

Variant	LiftOver Note	Raw Min	Raw Mean	Raw Max	Quantile Min	Quantile Mean	Quantile Max	Splicing Score

Variant	LLR Score	Interpretation

Variant	Score (L2)	Interpretation

Variant	Transcript ID	Gene	Score	Prediction

Variant	Transcript ID	Gene	Score	Prediction

Variant	LiftOver Note	Score

Variant	LiftOver Note	Score

Variant	LLR Score	Ref Score	Var Score	Interpretation	Context (bp)