mcp-ncbi-variationSAFE
dbSNP refSNP records and HGVS/SPDI/rsID normalization for human genetic variants, from NCBI Variation Services.
Overview
From the repository's own README, as read at the audited commit. Badges and raw HTML are left out.
dbSNP refSNP records and HGVS ↔ SPDI ↔ rsID normalization from NCBI Variation Services — the service that turns any spelling of a human genetic variant into the canonical coordinates the rest of genomics keys on.
Part of Pipeworx — an MCP gateway connecting AI agents to 1683+ live data sources.
Tools
variation_refsnp(rsid, assembly?, max_frequencies?)— the full refSNP
record: genomic placement on the build you ask for, HGVS genomic/transcript/ protein forms, SPDI, gene context, ClinVar clinical significance, and population allele frequencies (gnomAD, ExAC, 1000 Genomes, TOPMED, ALFA). Answers "what is rs113488022".
variation_hgvs_to_spdi(hgvs)— normalize an HGVS expression to contextual
SPDI alleles, and validate that the HGVS is well-formed at all.
variation_spdi_to_rsids(spdi)— the reverse: coordinate + alleles from a
VCF or pipeline → the rsIDs other databases key on.
Auth
Keyless. NCBI asks unauthenticated clients to stay under ~3 requests/second; the pack sends an identifying User-Agent.
Data sources
- — refSNP record.
- — HGVS → SPDI.
- — SPDI → rsIDs.
Traps
GRCh37 vs GRCh38 is the whole game. One refSNP carries placements on both builds at different coordinates — rs113488022 (BRAF V600E) is 7:140753336 on GRCh38 and 7:140453136 on GRCh37, 300kb apart. A caller who takes a coordinate from one build into a dataset annotated on the other gets "not found", which reads as "this variant does not exist". So assembly is an explicit argument (default GRCh38), every response states assembly_requested and assemblies_available, and an assembly with no placement says so in assembly_note instead of coming back as an empty array.
SPDI is 0-based, HGVS is 1-based. `NC_000007
6330c3ee78e2OBSERVED · 2026-10-11Connect
Built from this server's own package name, version and transport as found in its source — not copied from anyone's documentation, so it cannot drift against a page we do not control.
claude mcp add mcp-ncbi-variation -- npx -y @pipeworx/[email protected]
{
"mcpServers": {
"mcp-ncbi-variation": {
"command": "npx",
"args": [
"-y",
"@pipeworx/[email protected]"
]
}
}
}Exposed tools (3)
3 read · 0 write · 0 destructive.
| Tool | Risk | Description |
|---|---|---|
variation_hgvs_to_spdi | read | Normalize an HGVS expression to SPDI (sequence-position-deletion-insertion) contextual alleles via NCBI Variation Services. AUTHORITATIVE for turning a clinician- or paper-style variant string ( |
variation_refsnp | read | AUTHORITATIVE dbSNP refSNP record for a variant rsID, from NCBI Variation Services. PREFER OVER WEB SEARCH for |
variation_spdi_to_rsids | read | Look up the dbSNP rsIDs that a SPDI allele maps to, via NCBI Variation Services. AUTHORITATIVE for the reverse direction — you have a genomic coordinate and alleles from a VCF or a pipeline and need the rsID other databases key on. SPDI is 0-BASED, unlike HGVS: |
Trust audit
SAFEgrade B · trust 89/100 Nothing in the source contradicts what it says it does. Grade A is reserved for packages that have also passed the behavioural sandbox.
| Layer | What it checks | Result |
|---|---|---|
| L0 | Provenance & inventory | PASS |
| L1 | Static analysis of the code | PASS |
| L2 | Instruction surface (what it tells the agent) | PASS |
| L3 | Class-specific surface | PASS |
| L4 | Behavioural (sandbox) | SKIPPED |
What the source does
- Filesystem
- none-observed
- Network
- declared (1 observation(s))
- Shell
- none-observed
- Dependencies
- not all pinned
- Secrets in source
- none-found
Findings (1)
@modelcontextprotocol/sdk, tsx, typescript, @cloudflare/workers-types
Gates applied: no_behavioural_pass.
6330c3ee78e2full audit observations/trust-audit/mcp-server/pipeworx-io__mcp-ncbi-variation.json · Report an issue / request a re-scanAudit history
Every audit this server has had. A grade with a past is a grade somebody is still checking.
| Date | Source | Verdict | Grade | Score | Change |
|---|---|---|---|---|---|
| 2026-10-11 | 6330c3ee78e2 | SAFE | B | 89 | first audit |
Questions
What is the mcp-ncbi-variation MCP server?
dbSNP refSNP records and HGVS/SPDI/rsID normalization for human genetic variants, from NCBI Variation Services.
What tools does mcp-ncbi-variation expose?
3 in total: 3 read-only, 0 that write, and 0 that can delete or overwrite. Every one is listed on this page with its risk.
Is mcp-ncbi-variation safe to connect to an agent?
The audit found nothing in the source that contradicts what it says it does, and graded it B (89/100). Grade A is held back for packages that have also passed a sandboxed behavioural run, which is why a clean server reads B.
What credentials does mcp-ncbi-variation need?
No credential environment variables were found in its source, so it appears to need none.
How does mcp-ncbi-variation run?
It speaks stdio and streamable-http, so it runs as a local process your client starts. It is published on npm as @pipeworx/mcp-ncbi-variation at 0.1.1.
How current is this page?
The grade is for one exact copy of the source (6330c3ee78e2), read on 2026-10-11. The repository is watched and re-audited when it changes.