MCP server

GeneBe Official

net.genebe/genebe-mcp

Checked 26 Oct 2026, 08:29 UTC · Connected to it and listed its tools

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

Website Source

At a glance

Type

MCP server

Publisher

genebe.net (verified by the MCP Registry)

Status

Working at last check

Tools

6

Token cost

About 1,596 tokens per request

Sets up in

Claude Code, Claude Desktop, Codex, Gemini CLI, Cursor, VS Code, Antigravity, ChatGPT, OpenAI API, Grok

Last checked

26 Oct 2026, 08:29 UTC

Connect it to your agent

Add to CursorAdd to VS CodeVS Code Insiders

Opens the app, which shows the server and asks you to confirm. For other apps, copy the setup below.

Claude Code

claude mcp add --transport http genebe-mcp https://mcp.genebe.net/v1/mcp

Claude Desktop

Settings → Connectors → Add custom connector, and paste the URL.

Codex (config.toml)

[mcp_servers.genebe-mcp]
url = "https://mcp.genebe.net/v1/mcp"

Gemini CLI

{"mcpServers":{"genebe-mcp":{"httpUrl":"https://mcp.genebe.net/v1/mcp"}}}

Cursor

{"mcpServers":{"genebe-mcp":{"url":"https://mcp.genebe.net/v1/mcp"}}}

VS Code

{"servers":{"genebe-mcp":{"type":"http","url":"https://mcp.genebe.net/v1/mcp"}}}

Antigravity

agy mcp add genebe-mcp https://mcp.genebe.net/v1/mcp

ChatGPT

Settings → Apps & Connectors → Advanced settings: turn on Developer mode, then Create a connector and paste the URL. Which plans can do this varies.

OpenAI API (Responses tools)

{"type":"mcp","server_label":"genebe-mcp","server_url":"https://mcp.genebe.net/v1/mcp","require_approval":"always"}

Grok (xAI API tools)

{"type":"mcp","server_label":"genebe-mcp","server_url":"https://mcp.genebe.net/v1/mcp"}

Tools

• annotate_variant ~369 tokens
  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, ...)
• convert_variant ~227 tokens
  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.
• explain_acmg_decision_path ~341 tokens
  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 verdic
• get_gene ~190 tokens
  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.
• get_variant_effects ~199 tokens
  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.
• liftover_coordinate ~270 tokens
  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 warning

Browse

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