GeneBe MCP server

• Registry namenet.genebe/genebe-mcpverified in the MCP registry

The registry name sits under genebe.net. The registry only lets a publisher use that namespace after proving control of the domain through DNS or HTTP.

• Stateanswerschecked 2026-10-22
• Tools6
• Server calls itselfGeneBe
• Server version0.1.0
• Protocol version2025-06-18

On 2026-10-22 the server answered initialize and tools/list without a sign-in. First answer in 602 ms.

• Whether its tools do the product's job has not been judged yet.
• Checked on 6 of the 7 days it takes to judge reliability.

Said by rules from the measurements above. The likely first call is a model's pick from the tool list; read its description before relying on it.

• INITE MCP scoreafter a weeka score needs 7 daily checks: 6 so far
• Answeredmeasuring6 of the 7 daily checks it takes to print a share
• Median first answer748 ms
• Space in an agent's context≈ 1,396 tokensthe definitions of all its tools (6), which an agent carries on every turn
• Tool definitionsA · 100 of 100
• Typed results6 of 6 toolsdeclared outputSchema: results come typed, read once

• Every tool passes all six checks.

A program checks the server once a day: initialize and tools/list, no model. Tokens are the definitions' length at about four characters a token. The grade averages six checks of every tool's name, description, schema and annotations; it says how well the tools are described, not whether they work. The score weighs what was measured and nothing else: answering (25%), doing the product's job (25%), definitions (20%), context (10%), use (10%) and how readily a client connects (10%). A part that was not measured is left out, and a hidden instruction caps the score at 40. The state of vendors' MCP servers: method and numbers →

• 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…

• 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…

• 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…

• 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…

• 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…

• 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…