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AlphaGenome MCP Server

by taehojo
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TypeScript
Remote

explain_variant_impact

Explain a variant's predicted effects in plain language, reporting AVI score, top contributions, and strongest modality effects from AlphaGenome model predictions.

Instructions

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 source, and always stated in the result.

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"

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
altYesAlternate allele (A, C, G, T; more than one base for an indel)
refYesReference allele (A, C, G, T; more than one base for an indel)
sourceNoOptional: where the answer comes from (default: auto). auto = the precomputed AlphaGenome Atlas for single-nucleotide substitutions, live inference for everything else (indels, multi-nucleotide variants); falls back to live only when the Atlas does not hold the variant. atlas = Atlas only, errors instead of falling back. live = always run the model. The result always states which source answered.
scorersNoOptional: scorer names to use instead of the defaults. Names come from atlas_list_scorers and are the same for both sources, except the AVI scorers, which the Atlas alone serves.
positionYesGenomic position (1-based, hg38)
chromosomeYesChromosome (chr1-chr22, chrX, chrY)
tissue_typeNoOptional: 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.

  1. Changed7 schema fields changedv0.3.0
    • 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 / scorers
      Added value: +{
+  "description": "Optional: scorer names to use instead of the defaults. Names come from atlas_list_scorers and are the same for both sources, except the AVI scorers, which the Atlas alone serves.",
+  "items": {
+    "type": "string"
+  },
+  "type": "array"
+}
    • addedInput schema / properties / source
      Added value: +{
+  "description": "Optional: where the answer comes from (default: auto). auto = the precomputed AlphaGenome Atlas for single-nucleotide substitutions, live inference for everything else (indels, multi-nucleotide variants); falls back to live only when the Atlas does not hold the variant. atlas = Atlas only, errors instead of falling back. live = always run the model. The result always states which source answered.",
+  "enum": [
+    "auto",
+    "atlas",
+    "live"
+  ],
+  "type": "string"
+}
    • 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."
  2. First observed

TDQS

A3.7/5.0
Behavior4/5

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

With no annotations, the description carries the full disclosure burden and largely succeeds: it explains the auto/atlas/live dispatch, that atlas errors instead of falling back, that live always runs inference, that the source is always reported, and that no pathogenicity call is made and results are research-only. It does not cover latency, rate limits, or failure modes of live inference, but the safety/dispatch profile is well documented.

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?

The text is front-loaded (output shape first, then source routing, then disclaimers, then an example) and each paragraph earns its place. It is somewhat verbose and repeats the source-selection semantics that the schema already states, which is the only real redundancy.

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?

There is no output schema, so the description correctly carries the return-value burden by describing what the sentences contain and that the answering source is always stated. Combined with the parameter docs, an agent has enough to call and interpret the tool; only inter-tool routing against its many siblings remains unaddressed.

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 coverage is 100%, so all seven parameters are already documented, including the source enum and the note that scorer names come from atlas_list_scorers. The description restates the source behavior but adds no format, syntax, or defaulting detail beyond what the schema provides, so the baseline 3 applies.

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

Purpose4/5

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

The opening states a concrete verb and resource: it produces plain sentences restating a variant's predicted effects, and spells out exactly what those sentences contain (AVI score, biggest contributions, per-modality strongest effect with direction). It also carves out a distinct niche ('descriptive only... no statement about pathogenicity'), which separates it from assess_pathogenicity and related siblings. However, it never distinguishes itself by name from the many predict_* siblings that also report variant effects.

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

Usage Guidelines3/5

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

Usage is implied rather than stated. The description explains how the source is chosen and that it can be overridden, and gives an example prompt, but it never says when an agent should pick this narration tool over predict_variant_effect, generate_variant_report, or assess_pathogenicity. No explicit when-not guidance is offered.

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

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