GeneBe
REMOTE · MCP.GENEBE.NET
Annotate and classify human genetic variants with GeneBe (ACMG, gnomAD, ClinVar). Research use only.
Available components
Last scanned (8 hours ago)
Scores higher than 60% of remote servers
Reachable. Last reached 5 Nov 2026.
Category Health and Science
How this component scores in each security and reliability category. Every signal is checked automatically against the live server, and we only credit what we can confirm. How we score → Why this is hard to score →
Endpoint Security66
- The endpoint's TLS certificate is valid, in date, and uses a strong key. View diagnostics → Pass
- No authorisation is required to call this server. Every tool declares its destructiveHint and none is destructive, so open access doesn't expose one. See how to fix → View diagnostics → Partial
- HTTPS enforcement could not be verified: the plaintext port answered with HTTP 404, which proves neither a plaintext path nor enforcement. View diagnostics → Unverified
- HSTS check failed: the Strict-Transport-Security header is absent. See how to fix → View diagnostics → Fail
- DNSSEC is configured correctly; the domain's records validate against the full chain to the root. View diagnostics → Pass
Transport & Reachability100
- Verified streamable-http transport via a live MCP handshake. View diagnostics → Pass
Schema Quality & AI Usability68
- AI-judged instruction clarity (excellent).Pass
- Context-footprint check failed: tool/resource definitions use about 1124 tokens (~187/item across 6 items; 6 tools + 0 resources), over budget; trim descriptions and params. See how to fix → Fail
- Usage-examples check failed: none of the tools include examples. See how to fix → Fail
Stability & Change Management47
- Stability observed for 14 of 30 days with no destabilising changes; credit accrues until the full window elapses.Partial
Tool Coverage100
- 100% of tools have a non-trivial description (not blank, and not just the tool's name).Pass
- 100% of tool parameters carry a description.Pass
- Structured output schemas are declared (100% of tools); any adoption earns full credit.Pass
Tool Safety100
- No prompt-injection markers were found in the server instructions, tool names or descriptions we captured.Pass
- We read all 6 captured tool definition(s), and no name or description among them implies an irreversible operation.Pass
- An AI judge read all 7 captured unit(s) of tool text and found none that tries to manipulate the model reading it.Pass
Capabilities100
- Implements a current MCP spec version (2026-07-28).Pass
Every change we have recorded for this component, newest first. Security-relevant changes are always shown. ▲ marks a change for the better, ▼ a change for the worse; unmarked changes are neutral.
- 4 Nov 26 +1
No change was recorded against any check on this day. Stability & Change Management went from 40 to 43. That category is still filling its 30-day observation window: 12 days of observed history at the previous scan, 13 at this one. The score rises as the window fills, whether or not the server changes.
- 2 Nov 26 +1
No change was recorded against any check on this day. Stability & Change Management went from 33 to 37. That category is still filling its 30-day observation window: 10 days of observed history at the previous scan, 11 at this one. The score rises as the window fills, whether or not the server changes.
- 31 Oct 26 +1
- Server version: 0.1.0 → 0.1.1 functional
- 29 Oct 26 +1
No change was recorded against any check on this day. Stability & Change Management went from 20 to 23. That category is still filling its 30-day observation window: 6 days of observed history at the previous scan, 7 at this one. The score rises as the window fills, whether or not the server changes.
- 27 Oct 26 +1
No change was recorded against any check on this day. Stability & Change Management went from 13 to 17. That category is still filling its 30-day observation window: 4 days of observed history at the previous scan, 5 at this one. The score rises as the window fills, whether or not the server changes.
- 24 Oct 26 +1
No change was recorded against any check on this day. Stability & Change Management went from 3 to 7. That category is still filling its 30-day observation window: 1 days of observed history at the previous scan, 2 at this one. The score rises as the window fills, whether or not the server changes.
- 23 Oct 26 0
- Stability: unverified → 0.03 ▲ functional
- 22 Oct 26 67
First indexed and scored.
Diagnostic detail from the automated scan of this channel: what the scanner observed at each step, so you can see exactly where a check passed or failed. It is informational only and never changes the trust score.
Captured 5 Nov 2026 · Probed https://mcp.genebe.net/v1/mcp
TLS valid
Negotiated TLS 1.3 with TLS_AES_128_GCM_SHA256 .
| Subject | Issuer | Valid from | Valid until | Key | Signature | Serial |
|---|---|---|---|---|---|---|
| CN=genebe.net | CN=YE1,O=Let's Encrypt,C=US | 22 Oct 2026 | 20 Jan 2027 | ECDSA 256 | ECDSA-SHA384 | 6974c18f121edcc52a1185e4bd9b80a590f |
| SANs: api.genebe.net, docs.genebe.net, genebe.net, mcp.genebe.net, orchestrator.genebe.net, prifen.genebe.net, www.genebe.net | ||||||
| CN=YE1,O=Let's Encrypt,C=US (CA) | CN=Root YE,O=ISRG,C=US | 3 Sept 2025 | 2 Sept 2028 | ECDSA 384 | ECDSA-SHA384 | 5ddd70dd31f801c85c186a7a04b80afe |
| CN=Root YE,O=ISRG,C=US (CA) | CN=ISRG Root X2,O=Internet Security Research Group,C=US | 13 May 2026 | 2 Sept 2032 | ECDSA 384 | ECDSA-SHA384 | 872165fc34b6e5fba8add5b3705fb53a |
| CN=ISRG Root X2,O=Internet Security Research Group,C=US (CA) | CN=ISRG Root X1,O=Internet Security Research Group,C=US | 13 May 2026 | 2 Sept 2032 | ECDSA 384 | SHA256-RSA | 6c8f1dc727c7117f7baf853ac980f9cd |
Background: What to check on a remote MCP endpoint →
DNSSEC secure
Validation of mcp.genebe.net. — Secure
| Zone | DS | Keys | Algorithms | Outcome |
|---|---|---|---|---|
| . | trust_anchor | 20326, 38696 | 8, 8 | Verified |
| net. | present | 37331 | 13 | Verified |
| genebe.net. | present | 54824 | 8 | Verified |
| mcp.genebe.net. | Verified address RRset verified with the apex keys |
Authentication No authorisation required
The endpoint answered without asking for a token. Anyone who knows the URL can reach it.
| Result | No authorisation required |
|---|---|
| HTTP status | 200 |
Background: How OAuth 2.1 works in the 2026 MCP spec →
Transports 2 probes
| Transport | URL | Outcome | Status | Location |
|---|---|---|---|---|
| streamable-http | https://mcp.genebe.net/v1/mcp | Verified | 200 | |
| http (plaintext) | http://mcp.genebe.net/v1/mcp | Inconclusive | 404 |
The tools this component advertises to a client, with an estimated token cost for each. Expand a tool to see its parameters and schema. The per-tool counts are indicative and are not scored directly; the schema's total context footprint is one signal in Schema Quality & AI Usability. A tool's description is untrusted text the model reads on every call, which is what makes this list a security surface and not just an inventory: how tool poisoning works →
annotate_variant ~230
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.
| Name | Type | Req | Description |
|---|---|---|---|
| gene_symbol | – | – | Force this gene for the classification, e.g. TP53 |
| genome | string | – | Genome build of coordinate input. Ignored for HGVS/rsID. |
| transcript | – | – | Force this transcript for the classification, e.g. NM_000546.6 |
| variant | string | yes | The variant. Accepts 'chr-pos-ref-alt' (6-160585140-T-G), HGVS with transcript (NM_005577.4:c.4195A>C), rsID (rs41272110), SPDI, or 'GENE p.Thr1399Pro'. |
| Name | Type | Req | Description |
|---|---|---|---|
| clinvar | – | yes | – |
| consequences | array | yes | – |
| conservation | object | yes | – |
| dbsnp | – | yes | – |
| disclaimer | string | – | – |
| frequency | – | yes | – |
| gene | – | yes | – |
| links | – | yes | – |
| scores | – | yes | – |
| summary | – | – | Human-readable variant summary from GeneBe, when the backend provides one |
| total_consequences | integer | yes | – |
| truncated | boolean | – | – |
| variant | – | yes | – |
| verdict | – | yes | – |
| warning | – | – | – |
No examples provided.
convert_variant ~152
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.
| Name | Type | Req | Description |
|---|---|---|---|
| input_genome | string | – | Genome build of positional input (hg19 input is lifted to hg38). |
| variant | string | yes | HGVS (NM_007294.4:c.3756_3759del), rsID (rs429358), SPDI (NC_000007.14:11324573:C:T), 'chr-pos-ref-alt', or 'GENE p.Thr1700Ile'. |
| Name | Type | Req | Description |
|---|---|---|---|
| error | – | – | – |
| input | string | yes | – |
| variants | array | yes | Resolved hg38 coordinates (usually exactly one) |
No examples provided.
explain_acmg_decision_path ~205
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.
| Name | Type | Req | Description |
|---|---|---|---|
| genome | string | – | Genome build of coordinate input. |
| tree | string | – | Decision tree: 'germline' (default), 'oncogenicity' or 'acgs-uk-onco'. |
| variant | string | yes | The variant, in any notation accepted by annotate_variant. |
| version | string | – | Tree version: germline 2019 (default), oncogenicity 2022, acgs-uk-onco 2025. |
| Name | Type | Req | Description |
|---|---|---|---|
| disclaimer | string | – | – |
| text | string | yes | ASCII rendering of how each criterion was evaluated |
| tree | string | yes | – |
| truncated | boolean | – | – |
| variant | – | yes | – |
| version | string | yes | – |
No examples provided.
get_gene ~115
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.
| Name | Type | Req | Description |
|---|---|---|---|
| gene | string | yes | Gene symbol (BRCA1), alias, HGNC id (HGNC:1100), 'entrez:672' or Ensembl id (ENSG...). |
| include_transcripts | boolean | – | Also list the gene's transcripts. |
| Name | Type | Req | Description |
|---|---|---|---|
| alternative_hgnc_ids | array | – | – |
| chr | – | yes | – |
| end | – | yes | – |
| ensembl_id | – | yes | – |
| gene_disease_validity | array | yes | – |
| hgnc_id | – | yes | – |
| link | string | yes | – |
| mane_select_ensembl | – | yes | – |
| mane_select_refseq | – | yes | – |
| message | – | – | Set when an alias matched several genes |
| name | – | yes | – |
| ncbi_id | – | yes | – |
| omim_id | – | yes | – |
| start | – | yes | – |
| symbol | string | yes | – |
| total_gene_disease_entries | integer | yes | – |
| total_transcripts | integer | yes | – |
| transcripts | array | yes | – |
| truncated | boolean | – | – |
| uniprot_id | – | yes | – |
No examples provided.
get_variant_effects ~92
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.
| Name | Type | Req | Description |
|---|---|---|---|
| genome | string | – | Genome build of coordinate input. |
| variant | string | yes | The variant, in any notation accepted by annotate_variant. |
| Name | Type | Req | Description |
|---|---|---|---|
| effects | array | yes | – |
| total_effects | integer | yes | – |
| truncated | boolean | – | – |
| variant | – | yes | – |
No examples provided.
liftover_coordinate ~164
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.
| Name | Type | Req | Description |
|---|---|---|---|
| from_genome | string | yes | Genome build of the input. |
| query | string | yes | A position ('chr8:141310715'), an interval ('chr8:141310715-141310716') or a variant ('chr2-23423-A-C', HGVS, rsID). |
| to_genome | string | yes | Genome build to convert to. |
| Name | Type | Req | Description |
|---|---|---|---|
| candidates | array | yes | – |
| errors | array | yes | – |
| from_genome | string | yes | – |
| input | string | yes | – |
| status | string | yes | RESOLVED, AMBIGUOUS, UNRESOLVED, INVALID, NOT_RECOGNIZED or UNSUPPORTED |
| to_genome | string | yes | – |
| warnings | array | yes | – |
No examples provided.
How do I install the GeneBe MCP server?
GeneBe is a hosted endpoint at https://mcp.genebe.net/v1/mcp, so there is nothing to install locally. Ready-made configuration for Claude, Cursor, VS Code, Codex and 5 more is on this page, copied from each client's own documentation.
remote · mcp.genebe.net
claude mcp add --transport http net-genebe-genebe-mcp 'https://mcp.genebe.net/v1/mcp'
What is the GeneBe MCP server?
GeneBe is an MCP server listed in the public MCP registry as net.genebe/genebe-mcp. Annotate and classify human genetic variants with GeneBe (ACMG, gnomAD, ClinVar). Research use only. This page covers its hosted endpoint (https://mcp.genebe.net/v1/mcp).
Is the GeneBe MCP server safe to use?
GeneBe scores 73 out of 100 on VerifyMCP. That is a record of what we were able to check automatically, not an endorsement. The category breakdown on this page shows every signal behind the number, including the ones we could not confirm.
What tools does the GeneBe MCP server expose?
GeneBe exposes 6 tools: annotate_variant, explain_acmg_decision_path, convert_variant, get_variant_effects, get_gene, liftover_coordinate. Their descriptions and schemas cost roughly 958 tokens of context every time the server is loaded.
Does the GeneBe MCP server require authentication?
No. We connected to GeneBe without credentials and it answered, so anything it exposes is reachable by anyone who knows the address.
Is the GeneBe MCP server still maintained?
GeneBe is still listed as active in the MCP registry. We last reached this channel on 5 November 2026. Those dates come from our own scans of the registry and the channel itself, not from anything the publisher announced.