ClinVar Genetic Variants Scraper — Variant Pathogenicity Data
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from $3.00 / 1,000 results
ClinVar Genetic Variants Scraper — Variant Pathogenicity Data
Extract genetic variants from NCBI ClinVar. Filter by gene and pathogenicity. Get clinical significance, associated conditions, protein change, molecular consequence, and GRCh38 coordinates as JSON or CSV.
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from $3.00 / 1,000 results
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ClinVar Genetic Variants Scraper — Variant Pathogenicity API
Extract genetic variants and their clinical significance from NCBI ClinVar, the NIH public archive of relationships between human genetic variation and health. ClinVar is the reference database used by clinical geneticists, diagnostic labs, and pharmacogenomics teams worldwide — this Actor turns it into clean JSON, CSV, or Excel without writing a single Entrez query.
What you get
Each record is one ClinVar variant with the fields that matter for interpretation:
| Field | Description |
|---|---|
accession | ClinVar variation accession (e.g. VCV004856269) |
gene | Associated gene symbol (e.g. BRCA1, TP53) |
variantTitle | HGVS variant name (e.g. NM_004656.4(BAP1):c.687C>G (p.Asn229Lys)) |
clinicalSignificance | Germline classification — Pathogenic, Likely pathogenic, VUS, Benign, etc. |
associatedConditions | Disease / phenotype trait names linked to the variant |
proteinChange | Amino-acid change (e.g. N229K) |
molecularConsequence | Missense, nonsense, splice, intron variant, etc. |
reviewStatus | ClinVar review status / star rating context |
lastEvaluated | Date the classification was last evaluated |
variantType | SNV, deletion, duplication, etc. |
chromosome, start, stop, assembly | GRCh38 genomic coordinates |
canonicalSPDI | Canonical SPDI allele expression |
clinvarUrl | Direct link to the ClinVar variation page |
Why this matters
Variant interpretation is high-stakes and high-value: a single misclassified pathogenic variant can change a clinical decision. Use this Actor to:
- Build or refresh a variant knowledge base for a clinical/diagnostic pipeline
- Audit a gene panel (e.g. all pathogenic
BRCA1/BRCA2variants) - Power pharmacogenomics and research dashboards with structured variant data
- Feed RAG / LLM agents clean variant-condition relationships instead of raw XML
How to scrape ClinVar genetic variants
- Click Try for free.
- Set your filters:
- Gene Symbol — the gene to pull variants for (default
BRCA1). - Search Term — optional advanced Entrez query, combined with the gene using
AND. - Pathogenic / Likely Pathogenic Only — toggle to keep only actionable variants.
- Max Results — cap the run, or
0for every matching variant.
- Gene Symbol — the gene to pull variants for (default
- Click Start, then download as JSON, CSV, or Excel.
Example input
Example output
Pricing
This Actor uses pay-per-result pricing — a few cents for hundreds of fully-structured variant records, plus standard Apify compute. The Actor paces its requests to respect NCBI's public E-utilities rate limits.
FAQ
Where does the data come from? The official NCBI E-utilities API over the clinvar database. Only public ClinVar records are returned.
How fresh is the data? Live — each run queries NCBI directly, so newly submitted classifications appear immediately.
Can I query by disease instead of gene? Yes — use the Search Term field with an Entrez clause like breast cancer[disease].
Do I need an API key? No. The Actor uses the public, key-free E-utilities endpoints and self-throttles to stay within NCBI's fair-use limits.
Other Actors
Building a genomics or clinical data pipeline? Pair this with our other FDA, drug-label, and clinical-trial scrapers on the Apify Store.
Legal
This Actor retrieves only publicly available variant data from NCBI ClinVar. It does not access personal or patient data and respects NCBI's rate limits. You are responsible for using the output in compliance with NCBI's usage policies and applicable law.
