Gnomad
NPM · @PIPEWORX/MCP-GNOMAD · 2 COMPONENTS
gnomAD MCP — Broad Institute Genome Aggregation Database (GraphQL).
Available components
Last scanned (15 hours ago)
Scores higher than 65% of npm servers
Category Health and Science
How this component scores in each security and reliability category. Every signal is checked automatically from public evidence about the published package, including repeated runs of it in an isolated sandbox, and we only credit what we can confirm. How we score → Why this is hard to score →
Supply Chain Security100
- No malware found by supply-chain analysis.Pass
- No known CVEs affecting this package version or its production dependencies.Pass
- No install/post-install scripts declared.Pass
- No production dependencies, so there is no dependency health to assess. View diagnostics → Pass
Provenance & Transparency97
- Source repository is publicly reachable at the declared URL. View diagnostics → Pass
- Cryptographically verified build provenance (signed, bound to pipeworx-io/mcp-gnomad). View diagnostics → Pass
- Clear OSI-approved license (MIT).Pass
- Actively maintained (last published 3 days ago).Pass
- Disclosure check failed: no security disclosure policy was found in the source repository. See how to fix → Fail
Schema Quality & AI Usability59
- AI-judged instruction clarity (good).Pass
- Context-footprint check failed: tool/resource definitions use about 929 tokens (~185/item across 5 items; 5 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 Management23
- Stability observed for 7 of 30 days with no destabilising changes; credit accrues until the full window elapses.Partial
Tool Coverage87
- 100% of tools have a non-trivial description (not blank, and not just the tool's name).Pass
- 61% of tool parameters carry a description.Partial
Tool Safety100
- No prompt-injection markers were found in the server instructions, tool names or descriptions we captured.Pass
- We read all 5 captured tool definition(s), and no name or description among them implies an irreversible operation.Pass
- An AI judge read all 6 captured unit(s) of tool text and found none that tries to manipulate the model reading it.Pass
Capabilities100
- Implements a supported MCP spec version (2025-11-25); the latest is 2026-07-28.Pass
Checks we ran (16)
- Malware scan
- Known CVEs
- Install scripts
- Dependency health
- Source repository
- Provenance
- License
- Maintenance
- Security disclosure
- Schema quality
- Stability
- Tool coverage
- Injection markers
- Destructive annotations
- Judged manipulation
- MCP protocol
Does not apply to this package (2)
- Endpoint SecurityScored on hosted endpoints only. A package has no live endpoint of its own for us to probe.
- Transport & ReachabilityScored on hosted endpoints only. A package has no live endpoint of its own for us to probe.
The score does not measure everything. What the score does not measure →
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 17 to 20. That category is still filling its 30-day observation window: 5 days of observed history at the previous scan, 6 at this one. The score rises as the window fills, whether or not the server changes.
- 3 Nov 26 0
- Security disclosure: unverified → fail ▼ functional
- 2 Nov 26 +2
- Security disclosure: fail → unverified ▼ functional
- Stability: unverified → 0.13 ▲ functional
- Package version: 0.2.0 → 0.2.1 functional
- 29 Oct 26 77
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 · Analysed npm/@pipeworx/mcp-gnomad@0.2.1
Provenance Verified
A signed build attestation was found and verified, binding this exact artifact to the source repository it claims to come from.
| Result | Verified |
|---|---|
| Ecosystem | npm |
| Reason | Verified |
| Discovered via | Registry attestation endpoint |
| Source repo | pipeworx-io/mcp-gnomad |
| Certificate issuer | https://token.actions.githubusercontent.com |
| Certificate SAN | https://github.com/pipeworx-io/mcp-gnomad/.github/workflows/publish.yml@refs/heads/main |
| Rekor log index | 3637329412 |
| Predicate type | SLSA build provenance https://slsa.dev/provenance/v1 |
| Subject digest | sha512:aac068bf76cd239f1c92ed7b31ba925a6511a2b60f4beaf816d04a91628b39339f8ace199d7c48f664d3f09fab486d9d95ca8c1aed7daec76da205c0b |
Background: How many MCP packages publish verified provenance →
Dependencies 0 packages
| Packages resolved | 0 |
|---|---|
| Tree resolution | Complete |
Background: SBOMs and build attestations, explained →
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 →
gene ~165
Gene info + its variants. Accepts gene symbol (e.g. "BRCA1") or Ensembl gene id. Variants are paged (default 500, max 2,000 per call); variants_page gives the exact total and next_offset.
| Name | Type | Req | Description |
|---|---|---|---|
| dataset | string | – | – |
| gene_symbol_or_id | string | yes | – |
| limit | number | – | Variants to return, 1-2000. Default 500. gnomAD returns every variant with no limit of its own (BRCA1 has ~7,300), so the list is paged here; variants_page says how many exist and the next offset. |
| offset | number | – | Skip this many variants first, for the next page (variants_page.next_offset). Default 0. |
No output schema declared.
No examples provided.
region ~342
Variants in a genomic region (≤25kb recommended). You MUST say which genome build your start/stop are in via assembly — there is no default, because a position is valid in both builds and a wrong guess returns real variants from the wrong locus rather than an error. Variants are paged (default 500, max 2,000 per call); variants_page gives the exact total and next_offset.
| Name | Type | Req | Description |
|---|---|---|---|
| assembly | string | yes | REQUIRED. The genome build your start/stop are in: "GRCh38" (= hg38) or "GRCh37" (= hg19). There is no default, because every position is valid in both builds — an unstated build cannot be detected,… |
| chrom | string | yes | e.g. "1", "X", "MT" |
| dataset | string | – | Default gnomad_r4 (GRCh38). gnomad_r2_1* and exac are GRCh37. |
| limit | number | – | Variants to return, 1-2000. Default 500. gnomAD returns every variant with no limit of its own (BRCA1 has ~7,300), so the list is paged here; variants_page says how many exist and the next offset. |
| offset | number | – | Skip this many variants first, for the next page (variants_page.next_offset). Default 0. |
| start | number | yes | – |
| stop | number | yes | – |
No output schema declared.
No examples provided.
search ~68
Autocomplete-style search across gnomAD genes and variants by free-text query; returns matching Ensembl gene IDs with symbols, and matching variant IDs (an rsid resolves here). Use to resolve a partial gene name, symbol or rsid before calling gene or variant.
| Name | Type | Req | Description |
|---|---|---|---|
| query | string | yes | – |
No output schema declared.
No examples provided.
transcript ~188
Fetch gnomAD variant data for an Ensembl transcript (ENST…), returning transcript coordinates, gene symbol, chromosome position, and per-variant allele counts (ac/an) from exome and genome datasets. Variants are paged (default 500, max 2,000 per call); variants_page gives the exact total and next_offset.
| Name | Type | Req | Description |
|---|---|---|---|
| dataset | string | – | – |
| limit | number | – | Variants to return, 1-2000. Default 500. gnomAD returns every variant with no limit of its own (BRCA1 has ~7,300), so the list is paged here; variants_page says how many exist and the next offset. |
| offset | number | – | Skip this many variants first, for the next page (variants_page.next_offset). Default 0. |
| transcript_id | string | yes | Ensembl transcript id (ENST…) |
No output schema declared.
No examples provided.
variant ~111
Variant by chr-pos-ref-alt (e.g. "1-55051215-G-A") or rsid (e.g. "rs1801133"). Coordinates must match the dataset's genome build: the default gnomad_r4 is GRCh38, so a GRCh37/hg19 position will not be found — pass dataset "gnomad_r2_1" for GRCh37.
| Name | Type | Req | Description |
|---|---|---|---|
| dataset | string | – | Default gnomad_r4. |
| variant_id | string | yes | – |
No output schema declared.
No examples provided.
How do I install the Gnomad MCP server?
Gnomad runs locally as an npm package, launched with npx -y @pipeworx/mcp-gnomad. Ready-made configuration for Claude, Cursor, VS Code, Codex and 5 more is on this page, copied from each client's own documentation.
npm · @pipeworx/mcp-gnomad
claude mcp add pipeworx-io-gnomad -- npx -y @pipeworx/mcp-gnomad
What is the Gnomad MCP server?
Gnomad is an MCP server listed in the public MCP registry as io.github.pipeworx-io/gnomad. gnomAD MCP, Broad Institute Genome Aggregation Database (GraphQL). This page covers its npm package (@pipeworx/mcp-gnomad).
Is the Gnomad MCP server safe to use?
Gnomad scores 80 out of 100 on VerifyMCP. We found no known CVEs affecting it as of 5 November 2026. It declares no install or post-install scripts. Its build provenance is signed and verified. 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 Gnomad MCP server expose?
Gnomad exposes 5 tools: variant, gene, region, transcript, search. Their descriptions and schemas cost roughly 874 tokens of context every time the server is loaded.
Is the Gnomad MCP server still maintained?
Gnomad 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.
What licence is the Gnomad MCP server under?
Gnomad declares the MIT licence, which is OSI-approved. That covers the source only, and says nothing about the cost of any service it calls.
What did VerifyMCP test on the Gnomad MCP server?
VerifyMCP ran 16 checks on Gnomad, covering Malware scan, Known CVEs, Install scripts, Dependency health and 12 more. Endpoint Security and Transport & Reachability do not apply to an npm package, so they were not tested. The score does not measure everything, and the scoring documentation lists what it leaves out.