GeneBe MCP Server

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answering

GeneBe is answering right now. Last checked 1 min ago. It exposes 6 tools. Last commit 22 Oct 2026.

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

Uptime history 11 days of history

11 days agonow

100.0%

Uptime 24h

92 of 92 checks

Tools

read from the server

200 ms

Response time

average over 24h

Stars

last commit 22 Oct 2026

What changed 1

Every tool that appeared, vanished or quietly changed what it asks for. Recorded since 30 October 2026. No other catalogue keeps this.

30 Oct a tool changed version

Nothing serious here today

Today is the operative word: we check GeneBe every 15 minutes and re-read its code on every release. Watch it and you find out the day that stops being true.

Connect this server

Endpoint below is the one we actually reach during checks — not the one copied from a README. Last verified 1 min ago.

Claude Code Claude Desktop Codex Cursor VS Code

run in your terminal

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

Settings → Connectors → Add custom connector, then paste this address

https://mcp.genebe.net/v1/mcp

~/.codex/config.toml

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

.cursor/mcp.json

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

.vscode/mcp.json

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

Available tools 6

Read directly from the server with tools/list, grouped by what they act on. If a tool disappears, we record the date.

annotate

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, ...), ClinVar status, transcript consequences, and links to the GeneBe page to cite. Research use only; not a diagnosis.

convert

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.

explain

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 that annotate_variant returns; the somatic trees 'oncogenicity' (2022) and 'acgs-uk-onco' (2025) can be requested explicitly. Research use only.

gene

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

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 such as REF_MISMATCH may apply.

variant

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.

Endpoints

URL	Transport	State	Latency	Checked
https://mcp.genebe.net/v1/mcp	streamable-http	answering	204 ms	1 min ago

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GeneBe — questions

Answers built from our own checks of this server.

What can GeneBe do?

It exposes 6 tools, read directly from the server on our last check. Among them: annotate_variant, convert_variant, explain_acmg_decision_path, get_gene, get_variant_effects, liftover_coordinate. The full list with descriptions is on this page — we take it from the server itself via tools/list, not from a README. How MCP servers expose tools in the first place →

Is GeneBe working right now?

We send a real MCP handshake every 15 minutes. Over the last 24 hours 92 of 92 checks got a reply (100.0%), average response time 200 ms. The bar chart above shows every period we have measured.

How do I connect GeneBe?

Copy the ready config from this page. We generate it for Claude Code, Claude Desktop, Codex, Cursor and VS Code, each in the form that client actually reads. It is a remote server, so there is nothing to install — the client connects to the address.

Does GeneBe need an API key?

No. GeneBe completed a full MCP handshake with us as an anonymous client and listed its tools without asking for anything. All 6 of them are readable on this page. This is what we observed, not what the docs claim.

How fast is GeneBe?

It answers our handshake in 200 ms on average, which is faster than 71% of all working MCP servers we measure. The comparison comes from our own checks across the whole registry, every 15 minutes.

Is GeneBe open source?

The code is open source: it is published under the MIT licence, written in Python and 0 stars on GitHub. The licence covers the code in the repository, not the hosted service at mcp.genebe.net, which runs on its operator's own terms.