AlphaGenome MCP Server
Server Configuration
Describes the environment variables required to run the server.
| Name | Required | Description | Default |
|---|---|---|---|
| api-key | Yes | Your AlphaGenome API key from Google DeepMind |
Instructions
Guidance the server publishes about itself, which clients place ahead of the tool catalog so the model reads it before choosing anything.
This server publishes no instructions, or was last inspected before Glama recorded them.
Capabilities
Features and capabilities supported by this server
Protocol revision2025-11-25
| Capability | Details |
|---|---|
| tools | {} |
Tools
Functions exposed to the LLM to take actions
| Name | Description |
|---|---|
| predict_variant_effectA | Predicted regulatory effect of a genetic variant, per modality: the strongest tracks of each scorer (expression, transcription start, chromatin accessibility, histone marks, transcription factor binding, splicing), each with its score, calibrated quantile, gene, tissue or cell type, and assay. From the Atlas the AlphaGenome Variant Impact (AVI) score is included. Source: a single-nucleotide variant is answered from the precomputed AlphaGenome Atlas; an indel or multi-nucleotide variant runs live inference (score_variant). Both return the same scorers in the same shape. Chosen automatically, overridable with The response is a summary, never a full score matrix: ranked rows only, capped at top_n (default 25, max 100) and at 40,000 characters. Results are AlphaGenome model predictions for research prioritization, not clinical classifications: scores and calibrated quantiles are reported as returned, and no pathogenic/benign call is made. Example: "Analyze chr19:44908684 T>C with AlphaGenome" |
| batch_score_variantsA | Score up to 100 variants and rank them by predicted effect. Each variant is routed on its own: single-nucleotide variants to the Atlas, the rest to live inference. A mixed batch comes back as two separately ranked groups, because the Atlas group is ranked by the AVI score and live inference has no AVI score; the two must not be compared. The result reports how many variants came from each source and how many fell back. Scoring metric (used when Results are AlphaGenome model predictions for research prioritization, not clinical classifications: scores and calibrated quantiles are reported as returned, and no pathogenic/benign call is made. Example: "Score these 50 variants and show me the top 10 by predicted effect" |
| assess_pathogenicityA | Predicted effect size of a variant across modalities, for prioritization. The tool name is kept for compatibility: it does NOT classify a variant as pathogenic or benign, and Returns the strongest effect per scorer (score, calibrated quantile, where it was seen), the largest absolute quantile, and, for a single-nucleotide variant answered from the Atlas, the AlphaGenome Variant Impact (AVI) score. Source: a single-nucleotide variant is answered from the precomputed AlphaGenome Atlas; an indel or multi-nucleotide variant runs live inference (score_variant). Both return the same scorers in the same shape. Chosen automatically, overridable with Results are AlphaGenome model predictions for research prioritization, not clinical classifications: scores and calibrated quantiles are reported as returned, and no pathogenic/benign call is made. Example: "How large is the predicted effect of chr19:44908684 T>C?" |
| predict_tissue_specificA | The strongest predicted effect of a variant in each of several tissues: the same scores, filtered to the tracks of one tissue at a time. Runs live inference (score_variant with the SDK's recommended variant scorers); works for single-nucleotide variants, indels and multi-nucleotide variants. The result states Results are AlphaGenome model predictions for research prioritization, not clinical classifications: scores and calibrated quantiles are reported as returned, and no pathogenic/benign call is made. Example: "Compare the predicted effect of chr19:44908684 T>C in brain, liver and heart" |
| compare_variantsA | Two variants side by side: the strongest predicted effect of each modality for both, and which of the two has the larger absolute quantile per scorer. A comparison of predicted effect sizes, not of severity. Runs live inference (score_variant with the SDK's recommended variant scorers); works for single-nucleotide variants, indels and multi-nucleotide variants. The result states Results are AlphaGenome model predictions for research prioritization, not clinical classifications: scores and calibrated quantiles are reported as returned, and no pathogenic/benign call is made. Example: "Compare APOE rs429358 and rs7412" |
| predict_splice_impactA | Predicted splicing effects of a variant: splice sites, splice site usage and splice junctions, with the gene and junction of each. Runs live inference (score_variant with the SDK's recommended variant scorers); works for single-nucleotide variants, indels and multi-nucleotide variants. The result states Results are AlphaGenome model predictions for research prioritization, not clinical classifications: scores and calibrated quantiles are reported as returned, and no pathogenic/benign call is made. |
| predict_expression_impactA | Predicted gene expression effects of a variant: RNA-seq (log fold change per gene and tissue) and CAGE. Runs live inference (score_variant with the SDK's recommended variant scorers); works for single-nucleotide variants, indels and multi-nucleotide variants. The result states Results are AlphaGenome model predictions for research prioritization, not clinical classifications: scores and calibrated quantiles are reported as returned, and no pathogenic/benign call is made. |
| analyze_gwas_locusA | Rank the variants of a locus by predicted effect (largest absolute quantile across modalities), to prioritize candidates for follow-up. For single-nucleotide variants only, atlas_lookup_variants or atlas_scan_region is faster and adds the AVI score. Runs live inference (score_variant with the SDK's recommended variant scorers); works for single-nucleotide variants, indels and multi-nucleotide variants. The result states Results are AlphaGenome model predictions for research prioritization, not clinical classifications: scores and calibrated quantiles are reported as returned, and no pathogenic/benign call is made. |
| compare_allelesA | Rank the alternate alleles of one position by predicted effect. Runs live inference (score_variant with the SDK's recommended variant scorers); works for single-nucleotide variants, indels and multi-nucleotide variants. The result states Results are AlphaGenome model predictions for research prioritization, not clinical classifications: scores and calibrated quantiles are reported as returned, and no pathogenic/benign call is made. |
| batch_tissue_comparisonA | Rank several variants by predicted effect within each of several tissues: one ranking per tissue. Runs live inference (score_variant with the SDK's recommended variant scorers); works for single-nucleotide variants, indels and multi-nucleotide variants. The result states Results are AlphaGenome model predictions for research prioritization, not clinical classifications: scores and calibrated quantiles are reported as returned, and no pathogenic/benign call is made. |
| predict_tf_binding_impactA | Predicted transcription factor binding effects of a variant (TF ChIP-seq), with the factor and cell type of each. Runs live inference (score_variant with the SDK's recommended variant scorers); works for single-nucleotide variants, indels and multi-nucleotide variants. The result states Results are AlphaGenome model predictions for research prioritization, not clinical classifications: scores and calibrated quantiles are reported as returned, and no pathogenic/benign call is made. |
| predict_chromatin_impactA | Predicted chromatin accessibility effects of a variant (ATAC-seq and DNase-seq). Runs live inference (score_variant with the SDK's recommended variant scorers); works for single-nucleotide variants, indels and multi-nucleotide variants. The result states Results are AlphaGenome model predictions for research prioritization, not clinical classifications: scores and calibrated quantiles are reported as returned, and no pathogenic/benign call is made. |
| compare_protective_riskA | Two variants side by side, labelled as the caller names them. The tool compares predicted effect sizes per modality; it does not judge which allele is protective or a risk. Runs live inference (score_variant with the SDK's recommended variant scorers); works for single-nucleotide variants, indels and multi-nucleotide variants. The result states Results are AlphaGenome model predictions for research prioritization, not clinical classifications: scores and calibrated quantiles are reported as returned, and no pathogenic/benign call is made. |
| batch_pathogenicity_filterA | Keep the variants whose predicted effect reaches a threshold, ranked. The tool name is kept for compatibility: it filters on predicted effect size, NOT on pathogenicity, and classifies nothing.
Results are AlphaGenome model predictions for research prioritization, not clinical classifications: scores and calibrated quantiles are reported as returned, and no pathogenic/benign call is made. Example: "Which of these variants have a predicted effect above the 99.9th percentile?" |
| compare_variants_same_geneA | Rank several variants by their predicted effect on one gene. With gene_name, the gene-level scorers (RNA_SEQ, SPLICE_SITES) are restricted to that gene. Runs live inference (score_variant with the SDK's recommended variant scorers); works for single-nucleotide variants, indels and multi-nucleotide variants. The result states Results are AlphaGenome model predictions for research prioritization, not clinical classifications: scores and calibrated quantiles are reported as returned, and no pathogenic/benign call is made. |
| predict_allele_specific_effectsB | Predicted expression with the alternate allele against the reference allele: the RNA_SEQ scorer is that log fold change per gene and tissue, and RNA_SEQ_ACTIVE gives the expression level alongside it. Runs live inference (score_variant with the SDK's recommended variant scorers); works for single-nucleotide variants, indels and multi-nucleotide variants. The result states Results are AlphaGenome model predictions for research prioritization, not clinical classifications: scores and calibrated quantiles are reported as returned, and no pathogenic/benign call is made. |
| annotate_regulatory_contextA | The predicted effects of a variant across every regulatory modality at once: accessibility, histone marks, TF binding, CAGE, RNA-seq, splice sites, polyadenylation and contact maps. Shows where the predicted effect concentrates; it does not label the variant. Runs live inference (score_variant with the SDK's recommended variant scorers); works for single-nucleotide variants, indels and multi-nucleotide variants. The result states Results are AlphaGenome model predictions for research prioritization, not clinical classifications: scores and calibrated quantiles are reported as returned, and no pathogenic/benign call is made. |
| batch_modality_screenA | Rank several variants by predicted effect within one modality: expression (RNA_SEQ, CAGE), splicing (SPLICE_SITES, SPLICE_SITE_USAGE), tf_binding (CHIP_TF) or chromatin (DNASE, ATAC). Runs live inference (score_variant with the SDK's recommended variant scorers); works for single-nucleotide variants, indels and multi-nucleotide variants. The result states Results are AlphaGenome model predictions for research prioritization, not clinical classifications: scores and calibrated quantiles are reported as returned, and no pathogenic/benign call is made. |
| generate_variant_reportA | A fuller report of one variant's predicted molecular effects: more rows per scorer than predict_variant_effect and, from the Atlas, the AVI score with its feature attributions (AVI_SCORE_FEATURE_IMPORTANCE). It is a research summary, not a clinical report: it contains no pathogenicity classification and no recommendation. Source: a single-nucleotide variant is answered from the precomputed AlphaGenome Atlas; an indel or multi-nucleotide variant runs live inference (score_variant). Both return the same scorers in the same shape. Chosen automatically, overridable with The response is a summary, never a full score matrix: ranked rows only, capped at top_n (default 25, max 100) and at 40,000 characters. Results are AlphaGenome model predictions for research prioritization, not clinical classifications: scores and calibrated quantiles are reported as returned, and no pathogenic/benign call is made. Example: "Generate a report for chr19:44908684 T>C" |
| explain_variant_impactA | Plain sentences that restate a variant's predicted effects: the AVI score and its largest contributions (from the Atlas), then the strongest effect of each modality ordered by absolute quantile, with the direction for signed scorers. Descriptive only: the sentences restate returned numbers and make no statement about pathogenicity. Source: a single-nucleotide variant is answered from the precomputed AlphaGenome Atlas; an indel or multi-nucleotide variant runs live inference (score_variant). Both return the same scorers in the same shape. Chosen automatically, overridable with Results are AlphaGenome model predictions for research prioritization, not clinical classifications: scores and calibrated quantiles are reported as returned, and no pathogenic/benign call is made. Example: "Explain the predicted effect of chr17:49210289 C>T in plain language" |
| atlas_list_scorersA | List the variant scorers available in the AlphaGenome Atlas, including the AlphaGenome Variant Impact score (AVI_SCORE) and its feature attributions (AVI_SCORE_FEATURE_IMPORTANCE, AVI_SCORE_MODEL_FEATURES). Returns each scorer's name, number of tracks and the assays behind it. Use these names in the The Atlas holds precomputed AlphaGenome scores for single-nucleotide substitutions on the human reference genome (hg38, chr1-22, chrX, chrY). Indels and multi-nucleotide variants are not in it; use predict_variant_effect for those. |
| atlas_lookup_variantA | Look up the precomputed AlphaGenome scores of one single-nucleotide variant. No model call, so it answers in seconds. Returns, per scorer, the strongest tracks for the variant ranked by absolute score, each with its calibrated quantile, gene, tissue or cell type, and assay. Default scorers: AVI_SCORE plus one per modality (RNA_SEQ, CAGE, DNASE, CHIP_HISTONE, CHIP_TF, SPLICE_SITES). If the reference base does not match hg38, the Atlas says which base it expected and that message is returned as a validation error. The Atlas holds precomputed AlphaGenome scores for single-nucleotide substitutions on the human reference genome (hg38, chr1-22, chrX, chrY). Indels and multi-nucleotide variants are not in it; use predict_variant_effect for those. The response is a summary, never a full score matrix: ranked rows only, capped at top_n (default 25, max 100) and at 40,000 characters. Results are AlphaGenome model predictions for research prioritization, not clinical classifications: scores and calibrated quantiles are reported as returned, and no pathogenic/benign call is made. Example: "Look up chr19:44908684 T>C in the AlphaGenome Atlas" |
| atlas_lookup_variantsA | Look up precomputed AlphaGenome scores for up to 500 single-nucleotide variants in one call and rank them. Returns one row per variant (its strongest score and where it was seen), ranked. Default scorer: AVI_SCORE (AlphaGenome Variant Impact), one number per variant. With several scorers the ranking uses the largest absolute quantile. Variants the Atlas does not hold and variants it rejects (for example a reference base that does not match hg38) are listed separately with the reason; they do not fail the call. The Atlas holds precomputed AlphaGenome scores for single-nucleotide substitutions on the human reference genome (hg38, chr1-22, chrX, chrY). Indels and multi-nucleotide variants are not in it; use predict_variant_effect for those. The response is a summary, never a full score matrix: ranked rows only, capped at top_n (default 25, max 100) and at 40,000 characters. Results are AlphaGenome model predictions for research prioritization, not clinical classifications: scores and calibrated quantiles are reported as returned, and no pathogenic/benign call is made. Example: "Rank these 200 GWAS SNPs by their Atlas scores" |
| atlas_scan_regionA | Scan a genomic region in the AlphaGenome Atlas: every possible single-nucleotide substitution in the interval, ranked. Answers "which positions in this region matter most?" without running the model. Region width: at most 10,000 bp. Up to 50,000 bp only with allow_large_region=true. A scan is one API request per 32 bp under a requests-per-minute quota, so a large scan can take minutes. If the quota or the time limit stops a scan early, the partial result is returned, marked "Incomplete", with the range that was really scanned; the ranking then covers that range only. Default scorer: AVI_SCORE (about 7 seconds for 2,000 bp). Multi-track scorers are much slower (2,000 bp: DNASE 17 s, CHIP_TF 86 s). Scorers with one row per gene or junction (RNA_SEQ, SPLICE_JUNCTIONS, ...) cannot be used for a scan: scan with AVI_SCORE, then use atlas_lookup_variant on the top variants. The Atlas holds precomputed AlphaGenome scores for single-nucleotide substitutions on the human reference genome (hg38, chr1-22, chrX, chrY). Indels and multi-nucleotide variants are not in it; use predict_variant_effect for those. The response is a summary, never a full score matrix: ranked rows only, capped at top_n (default 25, max 100) and at 40,000 characters. Results are AlphaGenome model predictions for research prioritization, not clinical classifications: scores and calibrated quantiles are reported as returned, and no pathogenic/benign call is made. Example: "Scan chr17:49209289-49211289 and show the 10 substitutions with the largest predicted effect" |
Prompts
Interactive templates invoked by user choice
| Name | Description |
|---|---|
No prompts | |
Resources
Contextual data attached and managed by the client
| Name | Description |
|---|---|
No resources | |
TDQS
Scored across 24 tools
Several tools return essentially the same 'strongest effect per modality' summary — predict_variant_effect, assess_pathogenicity, annotate_regulatory_context, generate_variant_report and explain_variant_impact overlap heavily, differing mainly in verbosity. The comparison family (compare_variants, compare_alleles, compare_variants_same_gene, compare_protective_risk, batch_tissue_comparison) and the batch family (batch_score_variants, batch_modality_screen, batch_pathogenicity_filter, atlas_lookup_variants) also blur into each other. Legacy names that the descriptions explicitly disclaim (assess_pathogenicity, compare_protective_risk, batch_pathogenicity_filter) actively mislead selection.
All names are snake_case and almost all follow a verb_noun shape (predict_*, batch_*, compare_*, atlas_*, analyze_*, annotate_*, generate_*, explain_*). The atlas_* resource prefix and the varied verb set (predict/score/assess/analyze/compare/lookup/scan) are readable conventions rather than chaos. Minor deviation: some tools lead with an action while others lead with a scope prefix.
24 tools is on the heavy side for a variant-effect predictor, and a meaningful fraction are near-duplicates of a general scoring tool. Many could be folded into predict_variant_effect with parameters (modality, comparison mode, batch) without loss. The Atlas-vs-live distinction does justify some separate entries, but not this many.
The surface covers the full variant-scoring lifecycle: single variant, batch, region scan, Atlas lookup/list, per-modality breakdowns, tissue comparison, allele comparison and plain-language/narrative output. Gaps are minor — no non-variant sequence/annotation retrieval and no export/format options — but an agent can complete realistic prioritization workflows without dead ends.