# io.github.cyanheads/gnomad-genetics-mcp-server (remote · gnomad-genetics.caseyjhand.com)

Look up allele frequencies by ancestry, gene constraint, variants, and coverage over gnomAD.

- Trust score: 82/100 (high trust)
- Change this week: +3
- Registry status: active
- Liveness: live
- Owner verified: no
- Last scored: 2026-09-21

## Components

- remote · `gnomad-genetics.caseyjhand.com`: 82/100 (this document), [markdown](https://verifymcp.io/servers/cyanheads-gnomad-genetics-mcp-server/gnomad-genetics.md), [page](https://verifymcp.io/servers/cyanheads-gnomad-genetics-mcp-server/gnomad-genetics)
- npm · `@cyanheads/gnomad-genetics-mcp-server`: 43/100, [markdown](https://verifymcp.io/servers/cyanheads-gnomad-genetics-mcp-server/cyanheads-gnomad-genetics-mcp-server.md), [page](https://verifymcp.io/servers/cyanheads-gnomad-genetics-mcp-server/cyanheads-gnomad-genetics-mcp-server)

## Channel facts

- Endpoint: `https://gnomad-genetics.caseyjhand.com/mcp`
- Transports: `streamable-http`
- Auth: `none`
- Version: `0.2.2`

## Trust breakdown

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. Scores are 0–100 per category. Scoring method: https://verifymcp.io/docs/scoring (what has changed: https://verifymcp.io/docs/scoring/changelog)

Scored 2026-09-21.

- **Endpoint Security**: 66/100
  - The endpoint's TLS certificate is valid, in date, and uses a strong key.
  - Authorisation not fully verified: no authorisation is required to call this server, and 7 tool(s) never declared a destructiveHint. The MCP spec treats an absent hint as destructive by default, so we cannot call this surface safe.
  - HTTPS is enforced; there's no plaintext access path.
  - The HSTS (Strict-Transport-Security) header is present.
  - DNSSEC is configured correctly; the domain's records validate against the full chain to the root.
- **Transport & Reachability**: 100/100
  - Verified streamable-http transport via a live MCP handshake.
- **Schema Quality & AI Usability**: 76/100
  - 100% of prompts and resources have a non-trivial description (not blank, and not just the item's name).
  - AI-judged instruction clarity (excellent).
  - Context-footprint check failed: tool/resource definitions use about 2463 tokens (~351/item across 7 items; 7 tools + 0 resources), over budget; trim descriptions and params.
  - Usage-examples check failed: none of the tools include examples.
- **Stability & Change Management**: 100/100
  - No destabilizing schema changes in the last 30 days.
- **Tool Coverage**: 100/100
  - 100% of tools have a non-trivial description (not blank, and not just the tool's name).
  - 100% of tool parameters carry a description.
  - Structured output schemas are declared (100% of tools); any adoption earns full credit.
- **Tool Safety**: 100/100
  - No prompt-injection markers were found in the server instructions, tool names or descriptions we captured.
  - We read all 7 captured tool definition(s), and no name or description among them implies an irreversible operation.
  - An AI judge read all 8 captured unit(s) of tool text and found none that tries to manipulate the model reading it.
- **Capabilities**: 100/100
  - Implements a current MCP spec version (2026-07-28).

## Install

### How do I install the io.github.cyanheads/gnomad-genetics-mcp-server server?

io.github.cyanheads/gnomad-genetics-mcp-server is a hosted endpoint at https://gnomad-genetics.caseyjhand.com/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.

### Claude

```bash
claude mcp add --transport http cyanheads-gnomad-genetics-mcp-server 'https://gnomad-genetics.caseyjhand.com/mcp'
```

### Cursor

```json
{
  "mcpServers": {
    "cyanheads-gnomad-genetics-mcp-server": {
      "url": "https://gnomad-genetics.caseyjhand.com/mcp"
    }
  }
}
```

### VS Code

```json
{
  "servers": {
    "cyanheads-gnomad-genetics-mcp-server": {
      "type": "http",
      "url": "https://gnomad-genetics.caseyjhand.com/mcp"
    }
  }
}
```

### Codex

```toml
[mcp_servers.cyanheads-gnomad-genetics-mcp-server]
url = "https://gnomad-genetics.caseyjhand.com/mcp"
```

### opencode

```json
{
  "$schema": "https://opencode.ai/config.json",
  "mcp": {
    "cyanheads-gnomad-genetics-mcp-server": {
      "type": "remote",
      "url": "https://gnomad-genetics.caseyjhand.com/mcp",
      "enabled": true
    }
  }
}
```

### OpenClaw

```bash
openclaw mcp add cyanheads-gnomad-genetics-mcp-server --url 'https://gnomad-genetics.caseyjhand.com/mcp' --transport streamable-http
```

### Hermes

```yaml
mcp_servers:
  cyanheads-gnomad-genetics-mcp-server:
    url: "https://gnomad-genetics.caseyjhand.com/mcp"
```

### Netclaw

```json
{
  "McpServers": {
    "cyanheads-gnomad-genetics-mcp-server": {
      "Transport": "http",
      "Url": "https://gnomad-genetics.caseyjhand.com/mcp"
    }
  }
}
```

### Vellum

```bash
assistant mcp add cyanheads-gnomad-genetics-mcp-server -t streamable-http -u 'https://gnomad-genetics.caseyjhand.com/mcp'
```

### Other

```json
{
  "mcpServers": {
    "cyanheads-gnomad-genetics-mcp-server": {
      "type": "http",
      "url": "https://gnomad-genetics.caseyjhand.com/mcp"
    }
  }
}
```

The mcpServers block is a cross-client convention. Remote transports vary, so check your client's docs.

## Changelog

Every change recorded for this component, newest first. Days that predate change tracking, or that we cannot explain, say so: "we were watching and nothing happened" and "we were not watching" are different claims.

### 2026-09-21 (score 82, 0)

- [security] Stability: 0.97 → pass

### 2026-09-20 (score 82, +1)

- [functional] Server version: 0.2.1 → 0.2.2

### 2026-09-18 (score 81, +1)

No change was recorded against any check on this day. Stability & Change Management went from 87 to 90. That category is still filling its 30-day observation window: 26 days of observed history at the previous scan, 27 at this one. The score rises as the window fills, whether or not the server changes.

### 2026-09-16 (score 80, +1)

No change was recorded against any check on this day. Stability & Change Management went from 80 to 83. That category is still filling its 30-day observation window: 24 days of observed history at the previous scan, 25 at this one. The score rises as the window fills, whether or not the server changes.

### 2026-09-14 (score 79, +1)

No change was recorded against any check on this day. Stability & Change Management went from 73 to 77. That category is still filling its 30-day observation window: 22 days of observed history at the previous scan, 23 at this one. The score rises as the window fills, whether or not the server changes.

### 2026-09-12 (score 78, +1)

No change was recorded against any check on this day. Stability & Change Management went from 67 to 70. That category is still filling its 30-day observation window: 20 days of observed history at the previous scan, 21 at this one. The score rises as the window fills, whether or not the server changes.

### 2026-09-10 (score 77, +1)

No change was recorded against any check on this day. Stability & Change Management went from 60 to 63. That category is still filling its 30-day observation window: 18 days of observed history at the previous scan, 19 at this one. The score rises as the window fills, whether or not the server changes.

### 2026-09-07 (score 76, +1)

No change was recorded against any check on this day. Stability & Change Management went from 50 to 53. That category is still filling its 30-day observation window: 15 days of observed history at the previous scan, 16 at this one. The score rises as the window fills, whether or not the server changes.

## MCP tools (7)

### `gnomad_get_variant` (~332 tokens)

gnomad-genetics-mcp-server: get variant

Fetch the full gnomAD population record for one or more variants — allele count/number/frequency overall and broken down per genetic-ancestry group, homozygote and hemizygote counts, quality flags, transcript consequence, in-silico predictor scores, and joined ClinVar clinical significance. The "how common, is it benign" answer in one call. Accepts a batch of up to 25 IDs (chrom-pos-ref-alt or rsID) with per-item partial success: a malformed or absent ID lands in failed[] without failing the others. An empty found[] for a well-formed ID means the variant is not in the chosen dataset — pair with gnomad_get_coverage to confirm the position is callable before concluding true absence.
Data source: gnomAD (Broad Institute) — https://gnomad.broadinstitute.org/

Input parameters:

- `dataset` (string): gnomAD dataset: gnomad_r4 (GRCh38, default), gnomad_r3 (GRCh38), gnomad_r2_1 (GRCh37), exac (GRCh37). Echoed in output.
- `reference_genome` (string): Reference build. Derived from dataset when omitted (v4/v3=GRCh38, v2.1/ExAC=GRCh37). If supplied it must match the dataset, or the call is rejected. Keep aligned with ensembl coordinates.
- `variants` (array, required): 1–25 variant IDs (chrom-pos-ref-alt or rsID) to look up in one batched call.

Output parameters:

- `dataset` (string): Effective gnomAD dataset used for the batch.
- `error` (object): Present when the call failed. Absent on success.
- `failed` (array): Per-item failures: malformed IDs, variants absent from the dataset, or upstream errors.
- `found` (array): Variants resolved to a population record.
- `notice` (string): Non-fatal notice when optional ClinVar annotation was unavailable.
- `reference_genome` (string): Effective reference build used for the batch.

### `gnomad_get_gene_constraint` (~384 tokens)

gnomad-genetics-mcp-server: get gene constraint

Fetch gnomAD loss-of-function constraint for a gene — pLI (probability of LoF intolerance; >0.9 intolerant), LOEUF (oe_lof_upper, the headline metric; <0.6 intolerant in v4, <0.35 in v2) plus its lower bound, observed/expected ratios for LoF, missense, and synonymous variation, and the three Z-scores. This is the orthogonal axis to allele frequency: a loss-of-function variant matters far more in a gene intolerant to being broken. Accepts an HGNC symbol (PCSK9) or an Ensembl gene ID (ENSG00000169174). Many genes have null constraint (sparse upstream) — null fields are reported as such, never fabricated. v4 constraint is flagged beta by the gnomAD team; constraint_flags surfaces any caveats. Echoes the effective dataset and reference build.
Data source: gnomAD (Broad Institute) — https://gnomad.broadinstitute.org/

Input parameters:

- `dataset` (string): gnomAD dataset: gnomad_r4 (GRCh38, default), gnomad_r3 (GRCh38), gnomad_r2_1 (GRCh37), exac (GRCh37). Echoed in output.
- `gene` (string, required): Gene — HGNC symbol (e.g. PCSK9) or Ensembl gene ID (e.g. ENSG00000169174). Obtain a stable ID from ensembl_lookup_gene.
- `reference_genome` (string): Reference build. Derived from dataset when omitted (v4/v3=GRCh38, v2.1/ExAC=GRCh37). If supplied it must match the dataset, or the call is rejected. Keep aligned with ensembl coordinates.

Output parameters:

- `constraint_flags` (array): Constraint caveat flags (e.g. beta/experimental notes for v4).
- `dataset` (string): Effective gnomAD dataset.
- `error` (object): Present when the call failed. Absent on success.
- `exp_lof`: Non-negative expected LoF variant count. Null when unavailable.
- `exp_mis`: Non-negative expected missense count. Null when unavailable.
- `exp_syn`: Non-negative expected synonymous count. Null when unavailable.
- `gene_id` (string): Ensembl gene ID resolved for the gene.
- `lof_z` (number|null): LoF constraint Z-score. Null when unavailable.
- `mis_z` (number|null): Missense constraint Z-score. Null when unavailable.
- `obs_lof`: Non-negative observed LoF variant count. Null when unavailable.
- `obs_mis`: Non-negative observed missense count. Null when unavailable.
- `obs_syn`: Non-negative observed synonymous count. Null when unavailable.
- `oe_lof`: Non-negative observed/expected LoF ratio. Null when unavailable.
- `oe_lof_lower`: LOEUF confidence-interval lower bound. Null when unavailable.
- `oe_lof_upper`: LOEUF (oe_lof_upper) — the headline intolerance metric. Null when unavailable.
- `oe_mis`: Observed/expected missense ratio. Null when unavailable.
- `oe_syn`: Observed/expected synonymous ratio. Null when unavailable.
- `pli`: pLI — probability of LoF intolerance; >0.9 intolerant. Null when unavailable.
- `reference_genome` (string): Effective reference build.
- `symbol` (string): HGNC gene symbol.
- `syn_z` (number|null): Synonymous constraint Z-score. Null when unavailable.

### `gnomad_list_gene_variants` (~519 tokens)

gnomad-genetics-mcp-server: list gene variants

List every gnomAD variant in a gene, transcript, or region with allele frequencies and predicted consequences, optionally filtered to one consequence class (lof, missense, synonymous, other) and/or a maximum allele frequency. The full result is staged on a DataCanvas table named gene_variants and an inline preview is returned alongside canvas_id and table_name — run gnomad_dataframe_query against them to rank by AF, count by consequence, or group across the complete set rather than the preview. When the canvas is disabled (CANVAS_PROVIDER_TYPE != duckdb) the tool returns a capped inline preview with spilled=false and canvas_id empty; the SQL path is then unavailable. Supply exactly one of gene, transcript_id, or region. Echoes the effective dataset and build.
Data source: gnomAD (Broad Institute) — https://gnomad.broadinstitute.org/

Input parameters:

- `canvas_id` (string): Optional canvas ID from a prior call, to reuse the same canvas. Reusing it REPLACES (overwrites) the gene_variants table with this call's results — it does not append. Omit to start a fresh canvas; t…
- `consequence_class` (string): Keep only variants in this consequence class. Omit to return all classes.
- `dataset` (string): gnomAD dataset: gnomad_r4 (GRCh38, default), gnomad_r3 (GRCh38), gnomad_r2_1 (GRCh37), exac (GRCh37). Echoed in output.
- `gene` (string): Gene — HGNC symbol (e.g. PCSK9) or Ensembl gene ID (e.g. ENSG00000169174). Obtain a stable ID from ensembl_lookup_gene.
- `max_af` (number): Keep only variants with allele frequency ≤ this value (0–1). Variants with null AF are always kept.
- `reference_genome` (string): Reference build. Derived from dataset when omitted (v4/v3=GRCh38, v2.1/ExAC=GRCh37). If supplied it must match the dataset, or the call is rejected. Keep aligned with ensembl coordinates.
- `region`: Genomic region chrom-start-stop (1-based inclusive). Mutually exclusive with gene and transcript_id.
- `transcript_id` (string): Ensembl transcript ID (e.g. ENST00000302118). Mutually exclusive with gene and region.

Output parameters:

- `canvas_id` (string): Canvas ID — pass to gnomad_dataframe_query. Empty string when canvas is disabled.
- `dataset` (string): Effective gnomAD dataset.
- `error` (object): Present when the call failed. Absent on success.
- `notice` (string): Guidance when no variants matched, or when the canvas is disabled and the preview is capped.
- `preview` (array): Inline preview rows — the immediate answer.
- `reference_genome` (string): Effective reference build.
- `spilled` (boolean): True when the full result was staged on the canvas beyond the preview.
- `table_name` (string): Canvas table holding the full set (gene_variants); empty when not spilled.
- `total` (number): Total matching variants (staged row count when spilled, else preview length).

### `gnomad_get_coverage` (~412 tokens)

gnomad-genetics-mcp-server: get coverage

Fetch gnomAD sequencing-coverage summary across a gene, transcript, or region — mean and median read depth, plus the mean fraction of samples covered at each depth threshold (1× through 100×), separated by exome and genome track. Use this to disambiguate a true absent variant from an uncallable position: a variant missing from a well-covered region is informative, while one missing from a poorly-covered region is not. Supply exactly one of gene, transcript_id, or region. The optional coverage_source narrows to one track; by default both available tracks are returned. Echoes the effective dataset and build.
Data source: gnomAD (Broad Institute) — https://gnomad.broadinstitute.org/

Input parameters:

- `coverage_source` (string): Restrict to one coverage track. Omit to return every available track.
- `dataset` (string): gnomAD dataset: gnomad_r4 (GRCh38, default), gnomad_r3 (GRCh38), gnomad_r2_1 (GRCh37), exac (GRCh37). Echoed in output.
- `gene` (string): Gene — HGNC symbol (e.g. PCSK9) or Ensembl gene ID (e.g. ENSG00000169174). Obtain a stable ID from ensembl_lookup_gene.
- `reference_genome` (string): Reference build. Derived from dataset when omitted (v4/v3=GRCh38, v2.1/ExAC=GRCh37). If supplied it must match the dataset, or the call is rejected. Keep aligned with ensembl coordinates.
- `region`: Genomic region chrom-start-stop (1-based inclusive, e.g. 1-55039447-55064852). Mutually exclusive with gene and transcript_id.
- `transcript_id` (string): Ensembl transcript ID (e.g. ENST00000302118). Mutually exclusive with gene and region.

Output parameters:

- `dataset` (string): Effective gnomAD dataset.
- `error` (object): Present when the call failed. Absent on success.
- `notice` (string): Guidance when no coverage data is available for the target.
- `reference_genome` (string): Effective reference build.
- `summaries` (array): Per-track coverage summaries (exome and/or genome).
- `target` (string): The resolved target (gene symbol/ID, transcript ID, or region) the coverage describes.
- `target_kind` (string): Which target type was queried.

### `gnomad_search_clinvar` (~343 tokens)

gnomad-genetics-mcp-server: search clinvar

Search ClinVar (NCBI E-utilities) for a gene and return its classified variants — clinical significance, review status with a 0–4 star rating, associated conditions, molecular consequences, and submission counts — turning the variant-level significance gnomAD joins into a gene-panel curation view. Optionally filter by clinical_significance (e.g. pathogenic) and a minimum star rating. The full set is staged on a DataCanvas table named clinvar_variants with an inline preview; query it with gnomad_dataframe_query to rank or count across the complete set. Keyless, but honors NCBI_API_KEY for a higher rate limit. When the canvas is disabled the tool returns a capped inline preview with spilled=false. Credit: ClinVar, NCBI.

Input parameters:

- `canvas_id` (string): Optional canvas ID from a prior call, to reuse the same canvas. Reusing it REPLACES (overwrites) the clinvar_variants table with this call's results — it does not append. Omit to start a fresh canvas…
- `clinical_significance` (string): Filter by ClinVar clinical significance term (e.g. pathogenic, likely_pathogenic, benign).
- `gene` (string, required): Gene HGNC symbol (e.g. PCSK9). ClinVar indexes HGNC symbols only — Ensembl gene IDs (ENSG…) are not resolved here, unlike the other gnomAD tools; resolve one to its symbol via ensembl_lookup_gene.
- `min_review_stars` (integer): Keep only variants with at least this gold-star review rating (0–4).

Output parameters:

- `canvas_id` (string): Canvas ID — pass to gnomad_dataframe_query. Empty string when canvas is disabled.
- `error` (object): Present when the call failed. Absent on success.
- `notice` (string): Guidance when no ClinVar records matched, or when the canvas is disabled and the preview is capped.
- `preview` (array): Inline preview rows — the immediate answer.
- `spilled` (boolean): True when the full result was staged on the canvas beyond the preview.
- `table_name` (string): Canvas table holding the full set (clinvar_variants); empty when not spilled.
- `total` (number): Total matching ClinVar records (staged row count when spilled, else preview length).

### `gnomad_dataframe_query` (~182 tokens)

gnomad-genetics-mcp-server: dataframe query

Run a read-only SQL SELECT against a canvas table staged by gnomad_list_gene_variants (table gene_variants) or gnomad_search_clinvar (table clinvar_variants). Use the canvas_id and table_name those tools returned to rank by allele frequency, group by consequence class, count loss-of-function variants, or filter the full set the inline preview only sampled. SELECT statements only — writes, DDL, and file/HTTP table functions are rejected by the canvas gate. Call gnomad_dataframe_describe first to discover staged table and column names.

Input parameters:

- `canvas_id` (string, required): Canvas ID returned by gnomad_list_gene_variants or gnomad_search_clinvar.
- `sql` (string, required): Read-only SQL SELECT. Reference tables by the names the staging tool returned (e.g. gene_variants).

Output parameters:

- `columns` (array): Column names in the result, in order.
- `error` (object): Present when the call failed. Absent on success.
- `row_count` (number): Number of rows the query produced (materialized count).
- `rows` (array): Result rows (dynamic columns per the SQL projection), capped at the canvas row limit.
- `truncated` (boolean): True when the result exceeded the row cap and was clipped.

### `gnomad_dataframe_describe` (~107 tokens)

gnomad-genetics-mcp-server: dataframe describe

List the tables staged on a canvas and their columns (name and type) so you can write correct SQL for gnomad_dataframe_query. Use the canvas_id returned by gnomad_list_gene_variants or gnomad_search_clinvar. Returns one entry per table with its row count and column schema.

Input parameters:

- `canvas_id` (string, required): Canvas ID returned by a prior staging call (gnomad_list_gene_variants or gnomad_search_clinvar).

Output parameters:

- `error` (object): Present when the call failed. Absent on success.
- `tables` (array): Tables staged on the canvas.

## Diagnostics

Captured diagnostic sections: TLS, DNSSEC, Authorisation, Transports. The full working is on the page: https://verifymcp.io/servers/cyanheads-gnomad-genetics-mcp-server/gnomad-genetics#diagnostics

## Score history

- 2026-09-21: 82
- 2026-09-20: 82
- 2026-09-19: 81
- 2026-09-18: 81
- 2026-09-17: 80
- 2026-09-16: 80
- 2026-09-15: 79
- 2026-09-14: 79
- 2026-09-13: 78
- 2026-09-12: 78
- 2026-09-11: 77
- 2026-09-10: 77
- 2026-09-09: 76
- 2026-09-08: 76
- 2026-09-07: 76
- 2026-09-06: 75
- 2026-09-05: 75
- 2026-09-04: 74
- 2026-09-03: 74
- 2026-09-02: 73
- 2026-09-01: 73
- 2026-08-31: 72
- 2026-08-30: 72
- 2026-08-29: 71
- 2026-08-28: 71
- 2026-08-27: 70
- 2026-08-26: 70
- 2026-08-25: 68
- 2026-08-24: 67
- 2026-08-23: 67

## Common questions

### What is the io.github.cyanheads/gnomad-genetics-mcp-server server?

io.github.cyanheads/gnomad-genetics-mcp-server is listed in the public MCP registry as io.github.cyanheads/gnomad-genetics-mcp-server. Look up allele frequencies by ancestry, gene constraint, variants, and coverage over gnomAD. This page covers its hosted endpoint (https://gnomad-genetics.caseyjhand.com/mcp).

### Is the io.github.cyanheads/gnomad-genetics-mcp-server server safe to use?

io.github.cyanheads/gnomad-genetics-mcp-server scores 82 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 io.github.cyanheads/gnomad-genetics-mcp-server server expose?

io.github.cyanheads/gnomad-genetics-mcp-server exposes 7 tools: gnomad_get_variant, gnomad_get_gene_constraint, gnomad_list_gene_variants, gnomad_get_coverage, gnomad_search_clinvar, and 2 more. Their descriptions and schemas cost roughly 2,279 tokens of context every time the server is loaded.

### Does the io.github.cyanheads/gnomad-genetics-mcp-server server require authentication?

No. We connected to io.github.cyanheads/gnomad-genetics-mcp-server without credentials and it answered, so anything it exposes is reachable by anyone who knows the address.

### Is the io.github.cyanheads/gnomad-genetics-mcp-server server still maintained?

io.github.cyanheads/gnomad-genetics-mcp-server is still listed as active in the MCP registry. We last reached this channel on 21 September 2026. Those dates come from our own scans of the registry and the channel itself, not from anything the publisher announced.

## Links

- Remote endpoint: https://gnomad-genetics.caseyjhand.com/mcp
- Repository: https://github.com/cyanheads/gnomad-genetics-mcp-server
- Changelog RSS feed: https://verifymcp.io/servers/cyanheads-gnomad-genetics-mcp-server/gnomad-genetics.xml
- Changelog JSON feed: https://verifymcp.io/servers/cyanheads-gnomad-genetics-mcp-server/gnomad-genetics.json
- HTML version of this page: https://verifymcp.io/servers/cyanheads-gnomad-genetics-mcp-server/gnomad-genetics