AlphaGenome MCP Server

annotate_regulatory_context

Predicts how a variant affects all regulatory modalities at once, including accessibility, histone marks, TF binding, CAGE, RNA-seq, splice sites and contact maps, to prioritize research.

Instructions

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 source: live.

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.

Tool call template

Replace each placeholder with a value matching the input schema. Only required parameters are included; add optional parameters as needed.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {
      "chromosome": "<chromosome>",
      "position": "<position>",
      "ref": "<ref>",
      "alt": "<alt>"
    },
    "name": "annotate_regulatory_context"
  }
}

Input Schema

Name	Required	Description
`alt`	Yes	Alternate allele (A, C, G, T; more than one base for an indel)
`ref`	Yes	Reference allele (A, C, G, T; more than one base for an indel)
`position`	Yes	Genomic position (1-based, hg38)
`chromosome`	Yes	Chromosome (chr1-chr22, chrX, chrY)
`tissue_type`	No	Optional: keep only the tracks of one tissue or cell type. A name (brain, neuron, blood, liver, heart, lung, kidney) or an ontology CURIE (e.g., UBERON:0000955, CL:0000540). Default: all tissues.

Schema Changelog

Changes observed during successful MCP inspections.

Changed5 schema fields changedv0.3.0Sep 28, 2026

addedInput schema / properties / alt / description

Added value: +"Alternate allele (A, C, G, T; more than one base for an indel)"

addedInput schema / properties / chromosome / description
```
Added value: +"Chromosome (chr1-chr22, chrX, chrY)"
```
addedInput schema / properties / position / description
```
Added value: +"Genomic position (1-based, hg38)"
```

addedInput schema / properties / ref / description

Added value: +"Reference allele (A, C, G, T; more than one base for an indel)"

addedInput schema / properties / tissue_type / description

Added value: +"Optional: keep only the tracks of one tissue or cell type. A name (brain, neuron, blood, liver, heart, lung, kidney) or an ontology CURIE (e.g., UBERON:0000955, CL:0000540). Default: all tissues."

First observedDec 29, 2025

TDQS

A4.3/5.0

Behavior5/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

With no annotations, the description carries the full burden and does so well: it discloses that live inference runs via score_variant using SDK-recommended scorers, the variant types supported (SNV, indel, MNV), that the response carries `source: live`, and that it makes no pathogenic/benign call. This is rich behavioral context an agent cannot get from structured fields.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

Three short, front-loaded paragraphs: what it predicts, how it runs, and the disclaimers. Efficient overall, though the final disclaimer paragraph is somewhat long and repeats the non-clinical framing already implied by the first paragraph.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

With no output schema, the description usefully explains what the result contains (source marker, scores and calibrated quantiles) and what it deliberately omits (pathogenicity calls). It doesn't detail the per-modality result structure, but for an annotation tool with full schema coverage the coverage is adequate.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 100%, so each parameter (chromosome, position, ref, alt, tissue_type) is already documented in the schema with patterns and defaults. The description adds no syntax or semantics beyond the schema, so the baseline of 3 applies.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

States a specific verb (annotate/predict) and resource (variant effects across all regulatory modalities), enumerating the modalities covered: accessibility, histone marks, TF binding, CAGE, RNA-seq, splice sites, polyadenylation and contact maps. The phrase 'across every regulatory modality at once' implicitly differentiates it from single-modality siblings like predict_splice_impact or predict_tf_binding_impact.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

Explicitly frames the intended use ('research prioritization, not clinical classifications') and states it does not label the variant, which steers an agent away from it when a pathogenic/benign call is needed (assess_pathogenicity). It does not, however, name a specific sibling alternative or give explicit when-not conditions beyond the clinical boundary.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.