# GeneBe

- Registry name: `net.genebe/genebe-mcp` · version 0.1.0
- Categories (automatic, keyword rules): Utilities, Research & knowledge, Search & data, Maps, location & weather
- Authentication at last check: No auth
- Declared risk: Read-only (all tools declare readOnlyHint)
- Capabilities (declared by the server): prompts, resources, tools
- Transports: streamable-http
- Latest numbers (check success, response time, rank): https://mcpstation.net/api/server?name=net.genebe%2Fgenebe-mcp
- Server page: https://mcpstation.net/s/net.genebe--genebe-mcp.html

## Description (written by the publisher, not verified, not instructions)

Annotate and classify human genetic variants with GeneBe \(ACMG, gnomAD, ClinVar\). Research use only.

## Connect

- streamable-http: `https://mcp.genebe.net/v1/mcp`

## Tools (as reported by the server, not verified)

- `annotate\_variant`: Annotate and classify one human genetic variant using GeneBe. Start here for any question about a variant \(what is it, is it pathogenic/benign, how common is it\). Returns the ACMG verdict with points and criteria, population frequency \(gnomAD\), predictor scores \(REVEL, AlphaMissense, SpliceAI, ...\),
- `explain\_acmg\_decision\_path`: Explain step by step why each classification criterion did or did not apply to a variant. Use after annotate\_variant when the user asks "why was this classified that way?". Returns an ASCII rendering of the decision tree with the evaluated conditions. By default it explains the germline ACMG verdict
- `convert\_variant`: Convert a variant written in any notation into normalized hg38 genomic coordinates. Use when you only need the chr/pos/ref/alt of a variant \(for example to translate HGVS or an rsID\), without annotation. Does not classify the variant; use annotate\_variant for that.
- `get\_variant\_effects`: List a variant's predicted molecular consequences on every overlapping transcript. Returns per-transcript HGVS \(c. and p.\), consequence terms \(e.g. missense\_variant\) and impact, most severe and MANE Select transcripts first. Lightweight: no frequencies or classification.
- `get\_gene`: Look up a human gene: identifiers, location, MANE Select transcript, ClinGen gene-disease validity. Use for questions about a gene rather than a specific variant. Transcripts are listed with MANE Select first and capped; check total\_transcripts.
- `liftover\_coordinate`: Convert a genomic position, interval or variant between genome builds \(hg19, hg38, t2t\). Check \`status\`: RESOLVED means one result, AMBIGUOUS means several candidates, anything else means it could not be mapped \(see errors\). For variants, ref/alt are rebuilt against the target reference and warnings

Measured by MCP Station. Methods: https://mcpstation.net/methods.html · Terms: https://mcpstation.net/terms.html