// SCAN REPORT

AlphaGenome MCP Server

20 tools. 2 can modify or destroy data without limits.

2 write tools that can modify data. Rate limits recommended.

Last updated: 29 Jun 2026

2 can modify or destroy data

18 read-only

20 tools total

Community server · catalogue entry verified 29/06/2026

How to control AlphaGenome MCP Server ↓

TOOL MAP

What AlphaGenome MCP Server exposes to your agents

Read (18) Write / Execute (2) Destructive / Financial (0)

Running more than one server? Check your whole stack →

MOST DANGEROUS TOOLS

High Risk

The most dangerous AlphaGenome MCP Server tools

Execute · Medium batch_tissue_comparison This tool runs genomic analysis computations rather than simply retrieving static data (which would be Read). Execute · Medium predict_allele_specific_effects This tool executes complex bioinformatic algorithms (allele-specific effect prediction) whose outputs depend entirely on the input variants and parameters provided.

2 of AlphaGenome MCP Server's 20 tools can modify, destroy, or commit something on every call — and an agent calls them with no built-in limits.

POLICY

How to control AlphaGenome MCP Server

PolicyLayer is an MCP gateway — it sits between your AI agents and AlphaGenome MCP Server, and nothing reaches the server without passing your rules. These are the rules we recommend:

Cap read operations

{
  "analyze_gwas_locus": {
    "limits": [
      {
        "counter": "analyze_gwas_locus_per_minute",
        "window": "minute",
        "max": 60,
        "scope": "grant"
      }
    ]
  }
}

Controls API costs and prevents retry loops from exhausting upstream rate limits.

Create a free account and register AlphaGenome MCP Server — nothing to install.
Add these rules — paste them, or build them visually. Tune the limits to your setup.
Point your MCP client (Claude, Cursor, anything) at your gateway URL.

ENFORCE POLICY ON ALPHAGENOME →

Instant setup, no code required.

FULL CATALOGUE

All 20 AlphaGenome MCP Server tools

EXECUTE 2 tools

Execute batch_tissue_comparison Analyze multiple variants across multiple tissues. Efficient batch analysis of variants × tissues combination Execute predict_allele_specific_effects Analyze allele-specific regulatory effects. Detailed analysis of how each allele affects gene regulation diff

READ 18 tools

Read analyze_gwas_locus Analyze all variants in a GWAS locus. Ranks variants by regulatory impact for fine-mapping and causal variant Read annotate_regulatory_context Provide comprehensive regulatory annotation for a variant. Returns detailed regulatory context including all Read assess_pathogenicity Comprehensive pathogenicity assessment of a genetic variant. Evaluates variant across all regulatory modaliti Read batch_modality_screen Screen variants across specific regulatory modalities. Efficiently tests multiple variants for specific regul Read batch_pathogenicity_filter Filter variants by pathogenicity threshold. Efficiently identifies pathogenic variants from large lists. Per Read batch_score_variants Score and prioritize multiple genetic variants using AlphaGenome AI. Powered by Google DeepMind Read compare_alleles Compare different alleles at the same position. Useful for understanding effects of different mutations at a Read compare_protective_risk Compare protective vs risk alleles directly. Side-by-side comparison of alleles with opposite disease associa Read compare_variants Compare two variants side-by-side. Direct comparison of regulatory impacts between two variants. Returns: - Read compare_variants_same_gene Compare multiple variants within the same gene. Ranks variants by impact within a single gene context. Perfe Read explain_variant_impact Provide human-readable explanation of variant impact. Translates technical predictions into plain language. Read generate_variant_report Generate comprehensive clinical report for a variant. Full analysis with all modalities and clinical interpre Read predict_chromatin_impact Focus on chromatin accessibility effects only. Analyzes DNase and ATAC-seq predictions for chromatin state ch Read predict_expression_impact Focus on gene expression effects only. Analyzes RNA-seq and CAGE predictions for expression changes. Perfect Read predict_splice_impact Focus on splicing-specific effects only. Analyzes splice sites, splice site usage, and splice junctions. Per Read predict_tf_binding_impact Focus on transcription factor binding effects only. Analyzes TF binding site changes using ChIP-seq predictio Read predict_tissue_specific Predict variant effects across multiple tissues. Compares regulatory impact in different tissues to identify Read predict_variant_effect Predict the regulatory impact of a genetic variant using AlphaGenome AI. Powered by Google DeepMind

EXPLORE

Related servers

Other MCP servers with similar tools — same risk classification, starter policies for each.

FAQ

Questions about AlphaGenome MCP Server

Is the AlphaGenome MCP Server MCP server safe to use without restrictions? +

The AlphaGenome MCP Server server is primarily read-only with 18 read tools. While it cannot modify data, an agent in a retry loop can make thousands of API calls per minute, exhausting rate limits and running up costs. Rate limiting is still recommended.

How many tools does the AlphaGenome MCP Server MCP server expose? +

20 tools across 3 categories: Execute, Read, Write. 18 are read-only. 2 can modify, create, or delete data.

How do I enforce a policy on AlphaGenome MCP Server? +

Register the AlphaGenome MCP Server MCP server in PolicyLayer, apply the suggested rules above (adjust the limits to your use case), and point your AI client at the PolicyLayer proxy URL instead of the server directly. Your agents keep the same tools; PolicyLayer evaluates every call against policy before it executes. Nothing to install, live in minutes.

Enforce policy on every AlphaGenome MCP Server tool call.

Deterministic rules across all 20 AlphaGenome MCP Server tools. Per-identity grants. Full audit log. Live in minutes. Nothing to install.

ENFORCE POLICY ON ALPHAGENOME →

Instant setup, no code required.

20 AlphaGenome MCP Server tools catalogued and risk-classified — across an index of 43,000+ MCP servers.