AlphaGenome MCP Server

compare_variants_same_gene

Rank multiple variants by their predicted effect on a single gene, optionally restricting gene-level scorers to that gene. Use for research prioritization, not clinical classification.

Instructions

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 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": {
      "variants": "<variants>"
    },
    "name": "compare_variants_same_gene"
  }
}

Input Schema

Name	Required	Description	Default
`variants`	Yes	Variants to score (1-100)
`gene_name`	No	Optional: gene symbol (e.g., APOE)

Schema Changelog

Changes observed during successful MCP inspections.

Changed13 schema fields changedv0.3.0Sep 28, 2026
- changedInput schema / properties / gene_name / description
```
Previous value: -"Optional: gene name for context"New value: +"Optional: gene symbol (e.g., APOE)"
```
- addedInput schema / properties / variants / description
```
Added value: +"Variants to score (1-100)"
```
- addedInput schema / properties / variants / items / properties / alt / description
```
Added value: +"Alternate allele (A, C, G, T; more than one base for an indel)"
```
- addedInput schema / properties / variants / items / properties / alt / pattern
```
Added value: +"^[ATGCatgc]+$"
```
- addedInput schema / properties / variants / items / properties / chromosome / description
```
Added value: +"Chromosome (chr1-chr22, chrX, chrY)"
```
- addedInput schema / properties / variants / items / properties / chromosome / pattern
```
Added value: +"^chr([1-9]|1[0-9]|2[0-2]|X|Y)$"
```
- addedInput schema / properties / variants / items / properties / position / description
```
Added value: +"Genomic position (1-based, hg38)"
```
- addedInput schema / properties / variants / items / properties / position / minimum
```
Added value: +1
```
- addedInput schema / properties / variants / items / properties / ref / description
```
Added value: +"Reference allele (A, C, G, T; more than one base for an indel)"
```
- addedInput schema / properties / variants / items / properties / ref / pattern
```
Added value: +"^[ATGCatgc]+$"
```
- addedInput schema / properties / variants / items / properties / variant_id
```
Added value: +{
+  "description": "Optional: variant identifier (e.g., rs number)",
+  "type": "string"
+}
```
- addedInput schema / properties / variants / maxItems
```
Added value: +100
```
- changedInput schema / properties / variants / minItems
```
Previous value: -2New value: +1
```
First observedDec 29, 2025

TDQS

A3.8/5.0

Behavior4/5

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

With no annotations, the description carries the burden and does well: it discloses that inference is live, which variant types are supported (SNV, indel, MNV), that output carries source: live, and that results are research-grade model predictions with no clinical call. It omits operational traits like latency, rate limits, or auth requirements.

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 compact sentences, front-loaded with the core action before the gene-name behavior and the output/disclaimer detail. Every sentence contributes; the structure is clean and easy to scan.

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?

Since there is no output schema, the description usefully covers return semantics (ranking by predicted effect, source marker, calibrated quantiles reported as returned) and covers behavior in the absence of annotations. It could say more about the exact shape/ordering of the ranking result, but nothing critical is missing.

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

Parameters4/5

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

Schema coverage is 100%, so the baseline is 3, but the description adds real meaning beyond the schema by explaining that gene_name restricts the gene-level scorers (RNA_SEQ, SPLICE_SITES) to that gene, which the schema field ('Optional: gene symbol') does not convey.

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 description gives a specific verb+resource ('Rank several variants by their predicted effect on one gene') and adds technical scope (gene-level scorers RNA_SEQ, SPLICE_SITES). It does not explicitly name or distinguish itself from close siblings like compare_variants or compare_alleles, so an agent still has to infer the boundary.

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 only implied: the tool is scoped to ranking several variants within a single gene, and the gene_name clause hints at when the gene restriction applies. There is no explicit when-to-use, when-not-to-use, or routing to any of the many comparator siblings.

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