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GeneBe MCP server

online · 100% uptime
by genebe.net·net.genebe/genebe-mcp·v0.1.0
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Annotate and classify human genetic variants with GeneBe (ACMG, gnomAD, ClinVar). Research use only.

A87/100grade A
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Safety scan
A87/100

full report

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If you have run it, two minutes of your experience saves the next person an afternoon.

GeneBe tools (6)

write = sends, deletes, buys or posts
  • annotate_variantFree

    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_variantFree

    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_pathFree

    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.

  • get_geneFree

    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_effectsFree

    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_coordinateFree

    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.

Public scan report

scanner v0.1.10 · 2026-10-25 · same rubric, same numbers if you re-run it

no findings
  • –Code scanremote-only server, no package to scann/a
  • Live reliabilityremote reachable in 2019ms17/20
  • Tool poisoning6 tool descriptions checked15/15
  • Auth qualityopen endpoint, read-only tools10/15
  • Maintenancelast push 3 days ago15/15
  • Maintainer identitynamespace and repository owner differ; GitHub account older than a year; website matches verified namespace8/10
Overall 87/100. Components that don't apply are left out of the denominator. Any critical finding is an F.RubricAppeal a findingJSON

How GeneBe compares

Against every graded MCP server, from our own scans and uptime checks. Updated after each scan run.

Safety score
87/100
higher than 73% of 48,255 servers
Tools
6
the typical server has 7
Tools that change things
0%
typical: 0%. Fewer write tools means less an agent can break
Uptime
100%
of our recent checks; the typical remote server answers 100%
Response time
1,096 ms
faster than 10% of 30,031 servers

What its tools let an agent do: 6 read

Install GeneBe in Claude Code, Cursor or VS Code

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

What the publisher says

From the GeneBe repository's README, as published. We do not edit it. Read it on GitHub

🧬 GeneBe MCP

Give your AI assistant real variant-interpretation data instead of guesses.

Annotate and classify human genetic variants (ACMG, gnomAD, ClinVar, in-silico predictors) from Claude, Cursor, VS Code and any other MCP client, powered by GeneBe.

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

Why

Language models are bad at remembering the clinical status of a specific variant. They sound confident and are often wrong. GeneBe MCP lets the assistant look the variant up and answer from data: a transparent, points-based ACMG classification with every criterion explained, together with population frequencies, predictor scores, ClinVar and transcript consequences.

"Is NM005577.4:c.4195A>C benign?"*

"What is chr6-160585140-T-G? Explain why it is classified that way."

"Convert rs41272110 to hg38 and list its consequences on each transcript."

For example, chr6-160585140-T-G (rs41272110, LPA) comes back as Benign, −9 points with criteria BA1 and BP4, plus the data behind them and a link to the GeneBe page.

What you get

impact), gene details with MANE Select and ClinGen gene–disease validity.

  • Any notation in: genomic coordinates, HGVS, rsID or SPDI; hg19, hg38 and T2T supported through liftover.
  • Verdict you can audit: ACMG classification with points and the reasoning for each criterion, not a black-box label.
  • Evidence in one call: gnomAD frequencies, in-silico predictors, ClinVar, per-transcript consequences (HGVS c./p.,

structured data that follows the tool's output schema.

  • Compact answers: large lists are capped, so one call costs roughly 1–3k tokens, and every result also carries
  • Links back to GeneBe, so the human can check the source.

Connect in a minute

No sign-up, no API key. The server is remote; you only add its URL.

Claude Code

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

Claude (web and desktop)

Settings → Connectors → Add custom connector, then enter https://mcp.genebe.net/v1/mcp.

ChatGPT

Open chatgpt.com/plugins, click Add (+) → Add custom MCP, and enter https://mcp.genebe.net/v1/mcp.

Cursor

Add to ~/.cursor/mcp.json:

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

VS Code

Add to .vscode/mcp.json:

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

Any other client / try it with curl

Any client that supports remote MCP over Streamable HTTP works. Try it from a terminal:

curl -s -X POST https://mcp.genebe.net/v1/mcp \
  -H 'Content-Type: application/json' -H 'Accept: application/json, text/event-stream' \
  -d '{"jsonrpc":"2.0","id":1,"method":"tools/call","params":{"name":"annotate_variant","arguments":{"variant":"chr6-160585140-T-G"}}}'

More examples: USAGE.md.

Tools

Shortened. The full README is on GitHub.

Nothing above is checked by us. What we check is on the safety report.

GeneBe: common questions

Is GeneBe MCP server safe?
Yes, by our scan: it is graded A (87/100). Read the GeneBe safety report
How do I install GeneBe?
It runs remotely at mcp.genebe.net. Add it to Claude Code, Cursor, VS Code or Claude Desktop with the snippets above, or call it through the mcp.market gateway without installing anything.
Does GeneBe need an API key?
Not as far as the registry entry and our scan can tell: no credentials are declared or required.
Is GeneBe maintained?
The last commit was 13 days ago (2026-10-22). The latest release is v0.1.0.
Is GeneBe up?
100% of our last 28 checks got an answer. We check remote servers about four times a day.
How does GeneBe compare with other MCP servers?
safety score 87/100 (higher than 73% of 48,255 servers); tools 6 (the typical server has 7); tools that change things 0% (typical: 0%. Fewer write tools means less an agent can break). Full comparison.