NCBI ClinVar Variants Scraper

NCBI ClinVar Variants Scraper

Scrape genetic variant data from NCBI ClinVar by gene, condition, or any search term, up to a million per run. Each variant comes with its clinical significance, review status, associated conditions, and molecular consequence. No API key required. Export to CSV, JSON, Excel, or XML.

NCBI ClinVar is the central public archive of human genetic variants and their clinical interpretations, but browsing it manually or through the NCBI E-utilities API means dealing with XML parsing, rate limits, and complex pagination. This Actor reads the public ClinVar search results directly, filters by your search term, and returns each variant in one flat, analysis-ready row. It is built for researchers and clinicians who need structured variant data without writing a single line of code.

Who uses it	What they scrape NCBI ClinVar for
Clinical geneticists	Reviewing the clinical significance and evidence status of variants found in a patient panel.
Bioinformatics researchers	Building a local dataset of pathogenic variants for a specific gene family.
Pharma R&D teams	Identifying variants with conflicting interpretations that may be targets for functional studies.
Genetic counselors	Pulling the latest ClinVar submissions for a condition to prepare a patient report.

What it does

This Actor collects ClinVar variant records by gene, condition, or free-text search query and returns each one as a flat row with clinical significance, review status, and associated conditions.

• 🧬 Gene-centric search: enter a gene symbol like BRCA1 or TP53 to get all variants reported on that gene.
• 🩺 Condition-based search: use a disease name such as 'cystic fibrosis' to retrieve variants linked to that condition.
• 🔍 Free-text query: pass any ClinVar search string, including HGVS expressions or rsIDs, to target specific variants.
• 📊 Structured output: every row includes clinical significance, review status, last evaluation date, and associated conditions.

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

What you can do with NCBI ClinVar data

🧬 Build a gene-level variant catalog.

A clinical lab runs the Actor with a list of 50 cardiology-related genes and exports a CSV of all pathogenic and likely pathogenic variants for their internal knowledge base.

🩺 Monitor variant reclassifications.

A variant scientist scrapes the same gene every quarter, comparing review status and clinical significance to catch reclassifications that affect patient reports.

🔬 Feed a variant interpretation pipeline.

A bioinformatician pulls ClinVar data for a set of HGVS expressions and loads the JSON output into a custom annotation tool that merges it with population frequency data.

📋 Prepare a condition-specific report.

A genetic counselor searches for 'hereditary breast cancer' before a clinic day and exports the latest ClinVar submissions to share with patients during counseling sessions.

Why choose this scraper

	What you get
No API key	Reads the public ClinVar search pages directly, no NCBI account or API key registration.
Flat schema	Each variant is one row with consistent columns, ready for Excel, R, or Python pandas.
Up to 1M rows	Collect as many variants as your query returns, from a handful to a full gene panel.
Evidence included	Review status and last evaluation date come with every record so you can filter by confidence.

How it compares

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

	NCBI ClinVar Variants Scraper	Build it in-house	By hand
Setup	Run it now, zero config	Days of engineering	None, but hours per pull
When NCBI ClinVar 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 from a gene symbol, condition name, or any ClinVar search query, and set a maximum number of variants to collect so your dataset stays within the size you need. 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 ClinVar 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 ClinVar 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-clinvar-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 search query matches a term ClinVar recognizes. Try the exact gene symbol or condition name as it appears on the ClinVar website. Also verify that your maxItems is set to a number greater than zero.

The run is taking too long.

ClinVar can return thousands of variants for broad queries like a large gene. Reduce the 'Maximum variants' input to a smaller number, or narrow your search query to a more specific term.

Some fields are empty in my output.

Not every ClinVar record has all fields populated. For example, a variant may not have an associated condition or a molecular consequence listed. Empty cells mean ClinVar did not provide that data for that variant.

I got an error about the website structure changing.

NCBI occasionally updates the ClinVar page layout. If the Actor fails with a parsing error, please report it through the Actor's issue tracker so the selectors can be updated.

FAQ

Question	Answer
Do I need an NCBI API key to use this Actor?	No. The Actor reads the public ClinVar search results web pages directly, so no NCBI account or API key registration is required.
What search terms can I use?	You can use any term that works in the ClinVar search box: gene symbols like BRCA1, condition names like 'cystic fibrosis', HGVS expressions, or rsIDs.
How many variants can I collect in one run?	You set the maximum with the 'Maximum variants' input field, up to 1,000,000 per run. The Actor stops when it reaches that number or when ClinVar has no more results for your query.
What data fields does each variant row include?	Each row includes the variant name, gene, clinical significance, review status, last evaluation date, associated conditions, and molecular consequence, among other fields. The exact field list is visible in the sample output on the Actor's page.
Can I filter by clinical significance, like only pathogenic variants?	The Actor collects all variants matching your search query. To get only pathogenic variants, include 'pathogenic' in your search query, or filter the exported CSV or JSON in your own analysis tool.
Does this Actor handle variants with conflicting interpretations?	Yes. Variants where different submitters disagree on clinical significance are included, and the clinical significance field will reflect that conflict, such as 'Conflicting interpretations of pathogenicity'.
What export formats are supported?	You can export your dataset in CSV, JSON, Excel, or XML format from the Apify platform.
How often is the ClinVar data updated?	The Actor reads live data from the ClinVar website each time it runs, so you always get the latest submissions and reclassifications available at that moment.
Can I run this Actor on a schedule?	Yes. You can set up a scheduled run on Apify to scrape the same query daily, weekly, or monthly and receive notifications when new data is available.

Related actors

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.