English Français العربية

GeneBe

السجل الرسمي البحث والويب

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

الشيفرة المصدرية الموقع التوثيق

التثبيت

أضف هذا إلى إعدادات MCP في عميلك (Claude Desktop: claude_desktop_config.json، وCursor: ‏.cursor/mcp.json، ويستخدم VS Code وغيره الصيغة نفسها «mcpServers»).

Remote (streamable-http)
Claude Code 
claude mcp add --transport http genebe 'https://mcp.genebe.net/v1/mcp'
إعداد JSON (Claude Desktop وCursor وVS Code) 
{
    "mcpServers": {
        "genebe": {
            "type": "http",
            "url": "https://mcp.genebe.net/v1/mcp"
        }
    }
}

التوثيق

مأخوذ من ملف README للمشروع على GitHub ويُحدَّث أسبوعيًا. تفتح الروابط على GitHub.

المحتويات
  1. 🧬 GeneBe MCP
  2. Why
  3. What you get
  4. Connect in a minute
  5. Tools
  6. Trust and privacy
  7. Roadmap
  8. Data sources
  9. Contributing and self-hosting

🧬 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 NM_005577.4: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

  • 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., impact), gene details with MANE Select and ClinGen gene–disease validity.
  • Compact answers: large lists are capped, so one call costs roughly 1–3k tokens, and every result also carries structured data that follows the tool's output schema.
  • 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

ToolWhat it does
annotate_variantStart here. Any notation → ACMG verdict, points and criteria, frequencies, predictor scores, ClinVar, consequences, GeneBe links
explain_acmg_decision_pathWhy each classification criterion applied, in plain text
convert_variantHGVS / rsID / SPDI → hg38 coordinates
get_variant_effectsPer-transcript consequences (HGVS c./p., impact)
get_geneGene identifiers, location, MANE Select, ClinGen gene–disease validity, transcripts
liftover_coordinatePositions, intervals or variants between hg19 / hg38 / t2t

The default genome build is hg38.

Trust and privacy

  • Read-only. No tool changes anything, anywhere.
  • No account, no key needed to use the hosted server.
  • Single variants only. No patient data, no VCF files, no samples are sent or stored.
  • Nothing is stored and variant input is not logged by the MCP server.
  • Transparent classification. Results come from GeneBe's points-based ACMG implementation; the reasoning is returned with the verdict, so you and the assistant can check it.
  • Open source under the MIT license; you can read exactly what the server does, or run your own copy.
  • Research use only. This is not a medical device and not a diagnosis. Classifications must be reviewed by a qualified specialist before any clinical use.

Roadmap

Today GeneBe MCP answers questions about single variants. We plan to grow it into a workspace your assistant can use on your own data. None of the items below is available yet, and the order may change.

  • [ ] Sign-in, so the assistant can act on your GeneBe account
  • [ ] Your own samples: view and edit sample details and annotations
  • [ ] Search your cohort: find a variant across your own set of samples
  • [ ] Upload samples from the assistant
  • [ ] Supervise computations: start analyses, follow their progress and read the results

Ideas or requests? Open an issue or write to us via genebe.net.

Data sources

Results combine data from GeneBe, gnomAD, ClinVar, UniProt, ClinGen and dbNSFP predictors. Please check each source's license terms before redistributing the data.

Contributing and self-hosting

Want to run your own instance or change the code? See DEVELOPMENT.md. Issues and pull requests are welcome.

Made by the GeneBe team · MIT · Research use only

الأسئلة الشائعة

ما هو GeneBe؟

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

كيف أثبّت GeneBe؟

يعمل كخادم بعيد. في Claude Code: claude mcp add --transport http genebe 'https://mcp.genebe.net/v1/mcp'. وفي العملاء الآخرين، الصق إعداد JSON من هذه الصفحة في إعدادات MCP الخاصة بهم.

هل يحتاج GeneBe إلى مفتاح API؟

لا يذكر إدراجه في السجل أي مفتاح أو سر إلزامي. قد تتطلب بعض الميزات حسابًا لدى الخدمة التي يتصل بها.

هل GeneBe مفتوح المصدر؟

نعم. شيفرته متاحة على GitHub بترخيص MIT.

من يصون GeneBe؟

ينشره genebe-net. يدرجه AI.tn لكنه لا يصونه ولا يوصي به.

من سجل MCP الرسمي. الإدراج ليس توصية: راجع شيفرة الخادم وصلاحياته قبل منحه الوصول إلى بياناتك.