Genomic Prediction Tool

Single variant or batch VCF file prediction

Genome Version:

Select the reference genome version

🔑 AlphaGenome API key (optional — needed only for variants not already cached)

Remember on this device (stored in this browser only — never sent to us for storage)

Variants already in the MERGE precomputed cache are scored with AlphaGenome without a key. A variant that is not cached needs a live call to Google DeepMind's API, and that call is made under your key — we never spend a MERGE-owned key on your request. Without a key those variants simply come back with the AlphaGenome features marked unavailable; every other model still runs. Get a free key at deepmind.google.com/science/alphagenome.

The AlphaGenome API is provided for non-commercial use only and is subject to the AlphaGenome Terms of Service. Outputs generated by AlphaGenome should not be used for the training of other machine learning models.

Predictions are for theoretical modelling and research purposes only; they should not be used for clinical decision-making or relied upon for medical or other professional advice.

Select Models to Run:

AlphaGenome HyenaDNA NT Model AlphaMissense ESM-1b GPN-MSA popEVE Evo2 (Local) Enformer GENERATOR GENERATOR-v2 NT-v2 Carbon 🔬 Force SHAP plot generation (Skips rapid cache, ~10s per variant)

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)

🔑 AlphaGenome API key (optional — needed only for variants not already cached)

Remember on this device (stored in this browser only — never sent to us for storage)

The AlphaGenome API is provided for non-commercial use only and is subject to the AlphaGenome Terms of Service. Outputs generated by AlphaGenome should not be used for the training of other machine learning models.

Predictions are for theoretical modelling and research purposes only; they should not be used for clinical decision-making or relied upon for medical or other professional advice.

📧 Email Notification (Required)

Batch prediction runs on the server and results are always delivered by email (it can take a while for many variants). Enter your email and click Submit — you can safely close this page afterwards; we'll email you when the results are ready.

Results are sent to this address when processing completes.

Prediction Results

Variant:

⚠️ Multiple Transcripts Detected:

🧬 MERGE Pathogenicity Prediction

MERGE is the ensemble pathogenicity probability from the coding, splicing, non-coding, or non-SNV model. Its panels contain no AlphaGenome feature because AlphaGenome's official terms do not permit its outputs to be used as training features for machine-learning models.
MERGE-final combines MERGE with a calibrated single-feature AlphaGenome score (0.5 × MERGE + 0.5 × AlphaGenome) and uses its own interpretation bands. If AlphaGenome is unavailable, MERGE-final is reported as unavailable.
AlphaGenome is still fully extracted and displayed below; it feeds MERGE-final only.

ⓘ Note on two features (RTX 3090 hardware limits): evo2_1b_base is not among the computed features on this deployment, so it is median-imputed from the training distribution. carbon uses the same SUM log-likelihood-delta scoring as training, but over an 8 192 bp context window instead of the training's 24 576 bp (the larger window exceeds the 24 GB GPU memory). These two features are therefore approximate; all other features are computed exactly.

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.

Enformer Results

GENERATOR Results

GENERATOR-v2 Results

NT-v2 Results

Carbon Results

Carbon-3B, served by the local GPU gateway (SNV + non-SNV).

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Batch Prediction Results

Total Variants Processed

Total Transcripts Rendered

Variant (Chr:Pos Ref>Alt)	Transcript	Gene	🧬 MERGE Score	MERGE-final	AlphaGenome	HyenaDNA	NT Score	AlphaMissense	ESM-1b	GPN-MSA	popEVE	Evo2	Enformer	GENERATOR	GENERATOR-v2	NT-v2

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)

Variant	Score	Interpretation	Score Type

Variant	Score	Interpretation	Score Type

Variant	Score (L2)	Interpretation	Score Type

Variant	LiftOver Note	AbsMean	Mean	Std	Max Abs	Top5 AbsMean	Pos Sum	Neg Sum