Dbsnp Queries

What the source does

• FilesystemNone observedNo reads or writes in the source
• NetworkNone observedNo outbound calls in the source
• ShellNone observedNo commands run in the source
• DependenciesPinnedNothing floats
• SecretsNone foundNo keys in source

Five audit layers

Gates applied: no behavioural pass.

## Anticipated Reviewer Pushback

| Pushback | Standard response |

Audit 0.4.1 · source sha c8c1fc3a2b13 · 19 Oct 2026Report an issue or request a re-scan

• PublisherGPTomics GitHub organizationOwner of the repository this skill is read from
• Source folderGPTomics/bioSkills/clinical-databases/dbsnp-queriesThe exact folder we audited
• LicenceMITAs the repository states it
• Commit pinned for this verdictc8c1fc3a2b13A new audit runs when the source changes
• Repository statusArchivedLast push 65 days ago
• Sandboxed runNot runSkills are read, not executed; layer L4 is skipped

Its description: Resolves rsIDs, navigates RsMergeArch/SNPHistory merge chains, and converts between rsID, SPDI, HGVS, and VCF representations using the dbSNP Build 156 JSON architecture. Use when normalizing variant identifiers,…

---
name: bio-clinical-databases-dbsnp-queries
description: Resolves rsIDs, navigates RsMergeArch/SNPHistory merge chains, and converts between rsID, SPDI, HGVS, and VCF representations using the dbSNP Build 156 JSON architecture. Use when normalizing variant identifiers, joining variant databases by cluster ID, or tracking deprecated rsIDs through historical merges.
tool_type: python
primary_tool: myvariant
---

## Version Compatibility

Reference examples tested with: myvariant 1.0+, requests 2.31+, biopython 1.83+, Entrez Direct 21.0+. dbSNP Build 156 (September 2022) is the current schema; Build 151 (2017) was the last with relational SQL dumps. Builds 152-155 dual-released JSON+SQL; 156+ is JSON-only.

Before using code patterns, verify installed versions match. If versions differ:
- Python: `pip show <package>` then `help(module.function)` to check signatures
- CLI: `<tool> --version` then `<tool> --help` to confirm flags

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. The Variation Services REST API uses path-based versioning (`/variation/v0/`); E-utilities `db=snp` returns thin legacy summaries missing build-156 schema fields.

# dbSNP Queries and rsID Normalization

**'Look up this rsID / normalize variant representations'** -> Resolve rsIDs through merge chains, compute canonical SPDI, and convert between rsID, HGVS-g, HGVS-c, and VCF allele representations.

- Python (aggregator): `myvariant.MyVariantInfo().getvariant(rsid, fields=['dbsnp', 'clinvar', 'gnomad_exome'])`
- Python (direct): `requests.get(f'https://api.ncbi.nlm.nih.gov/variation/v0/refsnp/{rsid_int}')`
- Python (E-utilities, legacy): `Bio.Entrez.esearch(db='snp', term=rsid)`; returns thin summary
- Bulk: `ftp.ncbi.nlm.nih.gov/snp/latest_release/JSON/refsnp-chr{N}.json.bz2`

## rsID Is a Cluster Identifier, Not a Variant Identifier

This is the load-bearing concept. dbSNP cluster definition: ss records (submitted SNPs) are mapped to the genome and clustered into RefSNPs by *position + variant type*, not by allele. A single rsID can point to a *locus* with multiple alleles:

- `rs12345` may resolve to {A>G, A>T, A>C} at one position; the RefSNP JSON `primary_snapshot_data.placements_with_allele[*].alleles` enumerates them.
- ~6-8% of dbSNP rsIDs are multi-allelic.
- PLINK and many older tools historically misuse rsIDs as if they were variant identifiers, which fails for multi-allelic sites and yields wrong genotype assignments.

**Rule:** Use rsID as a *human-facing label only*; use SPDI or ClinGen Allele Registry CA ID for joins.

## Build 156 Schema Overhaul: What Changed

| Aspect | Build 151 (2017) | Build 156 (2022) and current |
|--------|------------------|------------------------------|
| Distribution | Relational SQL dumps + XML | JSON per RefSNP, partitioned by chromosome |
| FTP path | `ftp/snp/organisms/human_9606/` | `ftp.ncbi.nlm.nih.gov/snp/latest_release/JSON/` |
| Primary key | `snp_id`, `ss_id` | `refsnp_id`, with `primary_snapshot_data` block |
| Frequency data | Embedded sparse | ALFA aggregated populations |
| Merge tracking | `RsMergeArch.bcp.gz` | `refsnp-merged.json.bz2` (also `RsMergeArch.bcp.gz` retained for legacy) |
| Withdrawn | `SNPHistory.bcp.gz` | `refsnp-withdrawn.json.bz2` |
| API access | Legacy E-utilities `db=snp` only | Variation Services REST `/v0/refsnp/{id}` returns the full JSON |

E-utilities still works for `db=snp` but returns a thin pre-156 summary missing key fields like `primary_snapshot_data.placements_with_allele`; pipelines reliant on Entrez get out-of-date data.

## RsMergeArch: The Multi-Hop Merge Footgun

When two rsIDs are found to refer to the same allele cluster, the higher (later-assigned) rsID is merged into the lower. `RsMergeArch.bcp.gz` stores `(rsHigh, rsLow, rsCurrent)` tuples.

**The trap:** `rsCurrent` in any given row is the merge target at the time of that merge event, NOT the current dbSNP rsID. A multi-merge chain (rs3 -> rs2 -> rs1, then later rs1 -> rs0) appears as multiple rows. Naive one-hop lookup resolves to a stale ID.

Withdrawn rsIDs (submitter-withdrawn or QC-failed) live in `SNPHistory.bcp.gz`, not RsMergeArch. Both tables must be consulted to resolve any historical rsID.

## SPDI: The Canonical Variant Representation

SPDI (Sequence:Position:Deletion:Insertion) format: `NC_000017.11:43044294:G:A`. Position is **0-based, half-open** (differs from HGVS's 1-based, fully-closed).

The **Contextual Allele** transformation (Variant Overprecision Correction Algorithm) returns the right-aligned, normalized canonical form across left-aligned VCFs and right-aligned HGVS conventions. This is the basis for ClinGen Allele Registry CA ID computation.

| Representation | Build dependency | Transcript dependency | Bijective? | Best for |
|----------------|-----------------|----------------------|------------|----------|
| **VCF (chrom-pos-ref-alt)** | Yes | No | Yes (same build) | Pipelines, bulk |
| **SPDI** | Yes (via RefSeq accession) | No | Yes for SNV/small indel | Canonical normalization |
| **HGVS-g** | Yes (`NC_xxxxx.N`) | No | Yes for SNV/small indel | Human-readable genomic |
| **HGVS-c** | Indirect (via transcript) | Yes | No (one HGVS-c -> many HGVS-g) | Clinical reporting |
| **HGVS-p** | Indirect | Yes | Degenerate (one HGVS-p -> many HGVS-c) | Protein-level annotation |
| **rsID** | None (cluster identifier) | None | NO (multi-allelic) | Human label only |
| **CA ID** | None (canonical) | None | Yes | Cross-database join |

## Decision Tree by Query Scenario

| Scenario | Recommended path | Why |
|----------|------------------|-----|
| Resolve single rsID to coordinates + alleles | Variation Services `/v0/refsnp/{id}` | Returns full Build 156 JSON, including merge history |
| Resolve historical/deprecated rsID | Variation Services `/v0/refsnp/{id}` -> follow `merged_snapshot_data` chain | Single-hop RsMergeArch lookup misses m

Excerpt, first 6,000 characters of SKILL.md, verbatim from the audited commit. It is text from someone else’s repository, quoted so you can judge it before your agent reads it.

pip install myvariant biopython requests pandas

git clone https://github.com/GPTomics/bioSkills
git -C bioSkills checkout c8c1fc3a2b13

Works in

1. 2026-10-19
   !CAUTION B 89 / 100

   first audit · source c8c1fc3a2b13

Questions about Dbsnp Queries

• github.com/GPTomics/bioSkills/tree/main/clinical-databases/dbsnp — the audited source at commit c8c1fc3a2b13 and every finding aboveObserved · 19 Oct 2026

Spotted something wrong? Report a correction · Methodology