🧬 NCBI dbSNP Variants Scraper

🚀 Pull human SNP variants from NCBI dbSNP in seconds. rsIDs, chromosome and position, alleles, functional class, gene context, clinical significance and global minor allele frequencies from the official NIH database.

🕒 Last updated: 2026-05-27 · 📊 22 fields per record · 1B+ rsIDs · Global population frequencies

NCBI dbSNP is the world's authoritative public catalogue of single-nucleotide variants. This scraper wraps the official E-utilities esearch + esummary flow and returns a clean, structured table for any gene, condition or rsID query.

Every record carries the rsID, SPDI string, chromosome position, allele, functional class (intron/upstream/exon), gene symbols and Entrez IDs, validation status, clinical significance and global MAFs from 1000Genomes, gnomAD, TOPMED, TOMMO, ALFA and more.

🎯 Target Audience	💡 Primary Use Cases
Geneticists and bioinformaticians	Pull variant tables for a gene of interest
Clinical researchers	Build pathogenic-variant lists for a condition
Pharma and biotech	Annotate genotyping panels
Academic teams	Run reproducible analyses without flat-file pulls
Data engineers	Pipe dbSNP into your variant warehouse

📋 What the NCBI dbSNP Variants Scraper does

• Calls the official E-utilities esearch to resolve a gene/condition/rsID query
• Calls esummary to fetch full variant metadata
• Returns rsID, SPDI, chromosome, position, alleles, gene context, clinical significance, global MAFs
• Stream-delivers to multiple table outputs

💡 Why it matters: every clinical and pharmacogenomic analysis starts with annotating variants. dbSNP is the canonical source - and this actor makes it queryable from a spreadsheet workflow.

🎬 Full Demo (🚧 Coming soon)

⚙️ Input

Field	Type	Description
query	string	Gene symbol, rsID or condition keyword
maxItems	integer	Cap on records returned (free plan: 10)

{ "query": "BRCA1", "maxItems": 25 }

{ "query": "rs328", "maxItems": 1 }

⚠️ Good to Know: NCBI E-utilities is rate-limited to 3 requests/sec without an API key. The actor batches IDs into a single esummary call to stay well under the limit.

📊 Output

Field	Description
🆔 rsId	dbSNP rs identifier
🏷 snpClass	SNV / insertion / deletion / etc.
🧬 chromosome / position / accession / spdi	Genomic location
🔡 alleles	Allele code
📋 functionalClass	Intron / upstream / exon / etc.
🧪 geneSymbols / geneIds	Gene context
⚕️ clinicalSignificance	Benign / pathogenic / etc.
✅ validated	Validation status
📊 globalMaf / globalMafs	Global minor allele frequencies
🏷 handle / taxonomyId	Submitter and species
📅 createDate / updateDate / origBuild / updBuild	Provenance
📝 hgvs	HGVS notation
🔗 sourceUrl	dbSNP page
🕒 scrapedAt	ISO timestamp

✨ Why choose this Actor

• 🆓 Public NIH/NCBI data, no auth required
• 📡 Direct hit on the official E-utilities API
• 🧬 Returns global MAFs from 25+ populations
• 🧰 Clean field names - no feed parsing
• 📦 Pull as multiple table outputs

📈 How it compares to alternatives

Approach	Cost	Coverage	Setup time
Manual VCF pulls from NCBI FTP	Free	Bulk only	Hours
Direct E-utilities calls	Free	Full	Code required
ParseForge dbSNP Scraper	Pay-per-result	Full + structured	Minutes

🚀 How to use

1. Create a free Apify account (includes $5 credit).
2. Open the NCBI dbSNP Variants Scraper.
3. Set query (gene symbol, rsID or condition).
4. Click Start and use multiple table outputs.
5. Schedule or trigger from your bioinformatics pipeline.

💼 Business use cases

Pharmacogenomics - annotate a drug-response panel with current dbSNP records.

Clinical decision support - pull pathogenic variants for a condition.

Genotyping QC - verify variant annotations match the live dbSNP record.

Variant database curation - keep your internal warehouse in sync with NCBI updates.

🔌 Automating NCBI dbSNP Variants Scraper

Hook into Make, Zapier, n8n, Airbyte, Pipedream, Slack, GitHub Actions or any HTTP webhook.

🌟 Beyond business use cases

• Research: explore the global frequency of a candidate variant.
• Personal: annotate your own genotyping report from 23andMe / Ancestry.
• Non-profit: support rare-disease variant research.
• Experimentation: train ML models on annotated variant tables.

🤖 Ask an AI assistant about this scraper

Ask ChatGPT, Claude, Perplexity or Copilot: "How do I pull every pathogenic BRCA1 variant from NCBI dbSNP using the ParseForge Apify actor?"

❓ Frequently Asked Questions

Do I need an NCBI API key? No, but providing one increases your rate limit to 10 req/sec. The actor uses unauthenticated mode by default.

Is dbSNP human only? Currently human-focused. Other species are available via the same E-utilities pattern but with different taxonomyId.

Can I query by rsID directly? Yes - set query to rs328 or 328.

Are clinical-significance annotations from ClinVar? dbSNP propagates ClinVar annotations into the summary. Always verify in ClinVar for clinical use.

What's SPDI? The Sequence-Position-Deletion-Insertion notation: NCBI's modern standard for variant representation.

How fresh is dbSNP? dbSNP releases new builds periodically. The actor returns whatever the live API serves.

Can I get VCF output? This actor produces a tabular summary. Combine with NCBI's VCF use for raw genotyping.

Is the actor rate-limited? The actor stays under 3 req/sec to comply with E-utilities limits.

Are alternate assemblies supported? The actor returns the canonical GRCh38 position. Other assemblies require manual liftover.

Can I batch thousands of rsIDs? Yes - set maxItems accordingly. The actor batches into a single esummary call.

🔌 Integrate with any app

Apify, Make, Zapier, n8n, Pipedream, Slack, Airbyte, GitHub, Google Drive, Power Automate, AWS Lambda, REST webhook.

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💡 Pro Tip: browse the complete ParseForge collection for more government and research data scrapers.

🆘 Need Help? Open our contact form

⚠️ Disclaimer: independent tool, not affiliated with NCBI or NIH. Only publicly available open data is collected.