NCBI dbSNP Variants Scraper

NCBI dbSNP Variants Scraper

Scrape genetic variant data from NCBI dbSNP by gene symbol, rsID, or condition, up to a million per run. Each variant returns its rsID, alleles, clinical significance, and genomic location. No API key required. Export to CSV, JSON, Excel, or XML.

NCBI dbSNP is the central public archive for human genetic variation, but querying it manually across hundreds of variants is slow and error-prone. This Actor reads the public search results directly, letting you collect structured variant records for any gene, rsID, or disease term. It returns each matching variant in one flat, analysis-ready row.

Who uses it	What they scrape NCBI dbSNP for
Clinical geneticists	Compile a list of clinically significant variants for a gene panel from a single search term.
Bioinformatics researchers	Gather variant coordinates and allele frequencies for population studies without writing custom E-utilities scripts.
Pharma R&D teams	Monitor newly submitted variants linked to a disease target for drug discovery pipelines.

What it does

This Actor collects NCBI dbSNP variant records by free-text query and returns each one as a flat row with rsID, alleles, clinical significance, and genomic coordinates.

• 🔍 Free-text query: accepts gene symbols (BRCA1), rsIDs (rs334), or condition names (sickle cell).
• 📊 Flat row output: every variant is returned as one row, ready for spreadsheets or statistical tools.
• ⚙️ Configurable limit: set a maximum from 1 to 1,000,000 variants per run to control scope and cost.

Results export to CSV, JSON, Excel, or XML, or straight from the API.

What you can do with NCBI dbSNP data

🧬 Build a gene variant panel.

A clinical lab enters a gene symbol like BRCA1 and collects all linked variants with clinical significance to design a diagnostic report.

📈 Track variant submissions for a disease.

A researcher queries a condition like 'cystic fibrosis' weekly to capture newly submitted variants and update a research database.

🗺️ Retrieve genomic coordinates for annotation.

A bioinformatician searches by rsID list to get chromosome positions and alleles for a custom annotation track.

Why choose this scraper

	What you get
No API key or E-utilities setup	Query dbSNP directly without registering for an NCBI API key or managing rate limits.
Structured, flat schema	Every variant is returned with the same fields, so you can merge runs or load them into a database immediately.
Handles large queries	Collect up to a million variants in one run for genome-wide or panel-wide analyses.

How it compares

No other Store actor targets NCBI dbSNP the same way, so the honest comparison is with the alternatives teams actually weigh.

	NCBI dbSNP Variants Scraper	Build it in-house	By hand
Setup	Run it now, zero config	Days of engineering	None, but hours per pull
When NCBI dbSNP changes	Maintained for you	You fix it	You re-learn the page
Proxies, retries, anti-bot	Built in	Your problem	Browser only
Output	Fixed JSON schema, CSV/Excel export	Whatever you build	Copy-paste
Cost	Pay per result	Engineering time	Analyst hours

Configure the run

Drive the Actor with a single free-text query, and set a maximum variant count so only the records you need reach your dataset. The Input tab lists every parameter.

A first run with the defaults:

{
  "maxItems": 10
}

A larger pull:

{
  "maxItems": 200
}

Pricing

Pay-per-result: $0.021 per result collected. You pay only for the results written to your dataset.

Results collected	Approximate cost
100 results	$2.10
1,000 results	$21.00
10,000 results	$210.00

New Apify accounts start with $5 in free credit.

Free users

Free-plan runs return up to 10 results as a preview. Upgrade your Apify plan to collect up to 1,000,000 results per run.

Run it

1. Create a free Apify account with $5 in credit.
2. Open the NCBI dbSNP Variants Scraper.
3. Set your inputs and any filters, then click Start.
4. Export the results as CSV, Excel, JSON, or XML from the Dataset tab.

Run it programmatically through the Apify API (run-sync-get-dataset-items) or the ApifyClient for JavaScript and Python.

Use with AI agents (MCP)

Give an AI agent live access to NCBI dbSNP through the Model Context Protocol. Add the Actor to Claude, Cursor, or any MCP client:

$claude mcp add --transport http apify "https://mcp.apify.com?tools=parseforge/ncbi-dbsnp-variants-scraper"

Then prompt it in plain language to run the scraper and read back the results.

Troubleshooting

Why am I getting no results?

Check that your query matches a term that returns variants on the NCBI dbSNP website. Try the same search manually at ncbi.nlm.nih.gov/snp. If it returns results there, ensure your query is spelled correctly and does not contain extra punctuation.

The run stopped before collecting all variants.

Check the maxItems setting in your input. The Actor stops when it reaches that number. Increase the maximum if you need more variants, up to 1,000,000.

Some fields are empty in my dataset.

Not every variant has every field populated in dbSNP. For example, a variant may lack a clinical significance annotation. Empty cells mean the data was not present on the source page.

The run is taking a long time.

Large queries with high maxItems values will take longer because the Actor must paginate through many search results. Reduce maxItems or narrow your query to speed up the run.

FAQ

Question	Answer
What search terms can I use?	You can enter a gene symbol (BRCA1, APOE), an rsID (rs334, rs7412), or a condition name (sickle cell, cystic fibrosis). The query is passed directly to the dbSNP search, so any term that works on the website should work here.
Does this require an NCBI API key?	No. This Actor reads the public search results pages, so you do not need to register for an NCBI API key or manage E-utilities rate limits.
What fields are returned for each variant?	Each row includes the rsID, alleles, clinical significance, genomic location (chromosome and coordinates), and other metadata that dbSNP displays in its search results.
How many variants can I collect in one run?	You can set the maximum from 1 to 1,000,000 variants. The Actor will stop after reaching that count, even if the search returns more results.
Can I scrape multiple genes at once?	Each run takes a single query. To collect variants for multiple genes, run the Actor once per gene and merge the datasets afterward.
Is the data from the latest dbSNP build?	Yes. The Actor reads the live NCBI dbSNP website, so you always get the current build and the most recently submitted variants.
Can I filter by clinical significance inside the Actor?	The Actor returns all variants matching your query. You can filter the resulting dataset by clinical significance or any other field after the run using your own tools.
What output formats are supported?	You can export your dataset to CSV, JSON, Excel, or XML from the Apify platform.

Related actors

• google-scholar-scraper: Use this to find academic papers citing a variant or gene when you need citation data.

Browse the full ParseForge collection for more scrapers.

🆘 Need help? Email parseforge@protonmail.com with your run ID, your input, and what you expected.

⚠️ Disclaimer. This Actor is unofficial and is not affiliated with, endorsed by, or sponsored by National Center for Biotechnology Information, U.S. National Library of Medicine. It collects only publicly available data. You are responsible for using the collected data in compliance with the source's terms of service and applicable data-protection laws, including GDPR, CCPA, and PIPL. Do not use it to collect personal data unlawfully.