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/BRCA2 variants)
• 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

1. Click Try for free.
2. 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 0 for every matching variant.
3. Click Start, then download as JSON, CSV, or Excel.

Example input

{
  "geneSymbol": "TP53",
  "pathogenicOnly": true,
  "maxResults": 1000
}

Example output

{
  "accession": "VCV004856269",
  "gene": "BAP1",
  "variantTitle": "NM_004656.4(BAP1):c.687C>G (p.Asn229Lys)",
  "clinicalSignificance": "Likely pathogenic",
  "associatedConditions": "Tumor predisposition syndrome",
  "proteinChange": "N229K",
  "molecularConsequence": "missense variant; intron variant",
  "reviewStatus": "criteria provided, single submitter",
  "chromosome": "3",
  "start": "52406349",
  "assembly": "GRCh38",
  "clinvarUrl": "https://www.ncbi.nlm.nih.gov/clinvar/variation/4967194/"
}

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.