GeneBe

net.genebePublished by genebe.netOfficial publisherv0.1.0Updated Oct 26, 2026

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

VerifiedStreamable HTTPWeb executableData & AnalyticsAI & ML

Overview

AI-generated overview

Remote GeneBe server that lets an assistant annotate and classify human genetic variants with ACMG criteria, gnomAD frequencies, ClinVar and predictor scores.

What you can do
  • Annotate and classify a single variant: ACMG verdict with points and criteria, gnomAD frequencies, predictor scores, ClinVar and consequences
  • Explain step by step why each ACMG criterion did or did not apply, as a decision tree
  • Convert HGVS, rsID or SPDI notation into normalized hg38 coordinates
  • List per-transcript consequences with HGVS c./p. and impact
  • Look up a gene: identifiers, location, MANE Select transcript and ClinGen gene-disease validity
  • Lift positions, intervals or variants between hg19, hg38 and t2t
When to use it
Useful when a user asks about a specific human variant or gene and the assistant should answer from data rather than memory: what a variant is, whether it is pathogenic or benign, how common it is, or why it was classified that way.
Requirements
A remote MCP endpoint over Streamable HTTP; no sign-up, API key or environment variable is needed. Any MCP client that supports remote HTTP servers can connect. Network access to the hosted service is required.
Before you install
Research use only: it is not a medical device or a diagnosis, and classifications must be reviewed by a qualified specialist before clinical use. Variant input is sent to a third-party hosted service that combines GeneBe, gnomAD, ClinVar, UniProt, ClinGen and dbNSFP data; check each source's license before redistributing results. Tools are described as read-only and single-variant only, with no patient data, VCF files or samples.

Installation

In SourceWeft

  1. Open GeneBe in the dashboard and add it to a workspace.
  2. Enable the server for the chats that should use its tools.

Web executable via Streamable HTTP. Remote servers run from the web runtime once configured in a workspace.

Use with an agent

Paste this prompt into Claude Code, Codex, Cursor or another agent — or into SourceWeft chat. The agent reads this server's install guide, shows you its publisher, endpoint and sign-in, and adds it to your client once you agree. Keys never go into a command.

Read https://sourceweft.com/mcp/net.genebe%2Fgenebe-mcp/install.md and connect the MCP server it describes to my client. Before changing any config, show me its publisher, endpoint and sign-in method and wait for my OK. Never put an API key in a command or in a file I would commit; ask me where it should come from.

Read the install guide the agent follows

Other MCP clients

Add this to your client's mcpServers config.

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

README

🧬 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.

[License: MIT] [Transport] [Read only] [No account] [Research use only]

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
bash
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:

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

Add to .vscode/mcp.json:

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:

bash
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

Source: README.md at commit 521194f

Tools

6

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.

Parametersgenomevariantrequiredtranscriptgene_symbol

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.

Parameterstreegenomevariantrequiredversion

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.

Parametersvariantrequiredinput_genome

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.

Parametersgenomevariantrequired

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.

Parametersgenerequiredinclude_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 such as REF_MISMATCH may apply.

Parametersqueryrequiredto_genomerequiredfrom_genomerequired

Version history

1
  1. v0.1.0LatestOct 22, 2026

Score

100% of the applicable checks met

How complete this listing is, computed from the registry entry, the endpoint and public sources. Not a rating of the server and not a statement that it is safe or working today: reachability is a dated check, and no installs or reviews go into the score.

  • Reached in the last 30 daysRequired25 pts
  • Auth declaredRequired10 pts
  • Tools listedRequired15 pts
  • DescriptionRequired15 pts
  • Logo10 pts
  • Documentation15 pts
  • License10 pts