Query NCBI dbSNP for SNP records by rsID, gene, or region via E-utilities and Variation Services REST API. Retrieve alleles, MAF, variant class (SNV/indel/MNV), clinical links, cross-DB IDs (ClinVar, dbVar, 1000G). Free; 3 req/sec (10 with key). For clinical pathogenicity use clinvar-database; for population frequencies use gnomad-database.
SkillScore95Maintained
Automatic
◆Research pack
Last verified 8/24/2026
What it changes
Passed 21 of 22 test cases with the skill, and 10 of 22 without it.
Without skill45%
With skill95%
Checks it passed that the model alone missed
ESearch query combines CFTR[gene] with clinsig[filter].
Response specifies indel for insertion or deletion variants.
Code accesses the global_mafs key from the ESummary result record.
and 12 more in the full report
11 fixed10 passed either way1 still failing0 broke
Pass-rate lift
+50 pp
Tokens
+323%
Agent turns
0%
Response time
-27%
Model gemini-3.6-flashMeasured 8/24/2026v121 of 22 cases passed with skill
Tokens, turns and time describe resource use, not a dollar price.
See it in action
One of 11 test cases the skill fixed. Same model, same prompt, with and without the skill.
1 of 11
Prompt
In dbSNP ESummary records, what string value appears in the `snp_class` field for single nucleotide substitutions versus insertions or deletions?
What was checked, without and with the skill
Checked
Without skill
With skill
Response specifies snv for single nucleotide substitution variants.
Missed
Passed
Response specifies indel for insertion or deletion variants.
Missed
Passed
case-17 · gemini-3.6-flash · 8/24/2026 · answers are capped and redacted
What's inside
The instructions your model reads when the skill loads.
SKILL.md637 linessingle file
dbSNP Database
Overview
NCBI dbSNP is the primary public repository for short human genetic variants, cataloguing over 1 billion SNPs, indels, and MNVs with allele frequencies, functional annotations, and cross-references to ClinVar, gnomAD, and 1000 Genomes. Variants are identified by stable rsIDs (reference SNP cluster IDs). Access is free via two APIs: the legacy NCBI E-utilities and the newer NCBI Variation Services REST API, which returns structured JSON.
When to Use
Looking up allele frequencies and variant class for a known rsID
Searching all dbSNP variants in a gene or chromosomal region by name or coordinates
Resolving rsIDs to genomic coordinates (GRCh38/GRCh37) and HGVS notation
Checking whether a variant of interest has clinical significance links to ClinVar entries
Batch-fetching hundreds of rsIDs efficiently using epost+efetch history server
Cross-referencing a list of variant positions to dbSNP rsIDs for downstream annotation
For clinical pathogenicity classifications use clinvar-database; dbSNP provides IDs and frequency but not curated clinical significance
For population frequency stratified by ancestry use gnomad-database; dbSNP MAF is a single aggregate frequency
Data requirements: rsIDs (rs80357906), gene symbols, or chromosomal coordinates
Environment: internet connection; NCBI Entrez email required for E-utilities (set email parameter)
Rate limits: 3 requests/second without API key; 10 requests/second with free NCBI API key. Register at https://www.ncbi.nlm.nih.gov/account/ — add &api_key=YOUR_KEY to all requests
pip install requests pandas matplotlib
# xml.etree.ElementTree is part of Python stdlib — no additional install needed