ClinVar

free

ClinVar is a free, public NIH database aggregating reports of human genomic variants and their relationship to diseases and drug responses, with submissions from over 3,300 organizations in 95 countries.

Data & Analytics

Research & Education

Knowledge Management Tools

About

ClinVar is an official public database maintained by the National Center for Biotechnology Information (NCBI) at the U.S. National Library of Medicine. It serves as a centralized repository for information about genomic variants and their clinical significance, aggregating voluntary submissions from clinical testing laboratories, research labs, genetics clinics, patient registries, locus-specific databases, and expert panels across 95 countries. The database currently holds over 6.8 million submissions covering more than 4.4 million variants contributed by more than 3,300 submitters worldwide. ClinVar models its data through Variant-Condition (VCV) and condition-specific (RCV) records, enabling users to understand how multiple independent submissions for the same variant are aggregated and interpreted. Key capabilities include advanced search by gene, variant, genomic location (GRCh38/GRCh37), and disease term; downloadable bulk data via FTP; and a RESTful API for programmatic access. ClinVar supports HGVS expressions, data validation standards, and standardized review status and assertion criteria for clinical classification. ClinVar is primarily used by clinical geneticists, bioinformaticians, researchers, and healthcare professionals who need to assess the pathogenicity of genomic variants in the context of inherited disease and pharmacogenomics. It is not intended for direct diagnostic use without review by a genetics professional, but it is an indispensable reference for variant curation and genomic medicine workflows.

Key Features

Comprehensive Variant Archive: Aggregates over 6.8 million submissions covering 4.4 million+ human genomic variants from more than 3,300 submitters across 95 countries.
Advanced Search Interface: Search by gene, variant, genomic location (GRCh38/GRCh37), disease term, or other fields to quickly find clinically relevant variant data.
Programmatic API Access: Supports RESTful API and FTP bulk downloads, enabling bioinformaticians to integrate ClinVar data into custom pipelines and tools.
Standardized Clinical Classification: Uses HGVS expressions, defined review statuses, and assertion criteria to ensure consistent and interpretable variant classification.
VCV and RCV Record Model: Organizes data into Variant-Centric (VCV) and Condition-Specific (RCV) records, showing how multiple submissions for a variant are aggregated and contextualized by condition.

Use Cases

Clinical geneticists looking up the pathogenicity classification of a patient's variant to support genetic counseling and diagnosis.
Bioinformaticians building automated variant annotation pipelines that programmatically query ClinVar via API to flag clinically relevant variants.
Researchers studying the landscape of variants associated with a specific inherited disease or pharmacogenomic response.
Clinical laboratories submitting their variant interpretations to contribute to the global knowledge base and gain expert panel review.
Academic educators and students using ClinVar as a reference resource to learn about genomic variant classification and clinical genomics.

Pros

Completely Free and Publicly Accessible: ClinVar is an open, government-funded resource with no cost barriers, making it available to researchers, clinicians, and developers worldwide.
Large and Growing Dataset: With over 6.8 million submissions from thousands of global organizations, ClinVar offers one of the most comprehensive collections of clinically interpreted genomic variants available.
Flexible Data Access: Supports web search, FTP bulk downloads, and a programmatic API, accommodating a wide range of users from clinicians to bioinformaticians.
Authoritative and Standardized: Backed by NIH/NCBI and built around standardized data models, HGVS nomenclature, and expert panel curation, ensuring high data reliability.

Cons

Not for Direct Clinical Decision-Making: ClinVar explicitly states its data should not be used for direct diagnosis or medical decisions without review by a qualified genetics professional.
Data Quality Varies by Submitter: Because submissions are voluntary and not independently verified by NIH, the quality, completeness, and interpretation can vary across submitters.
Steep Learning Curve for Non-Specialists: Understanding HGVS expressions, VCV/RCV record structures, review statuses, and assertion criteria requires domain knowledge in clinical genetics or bioinformatics.

Frequently Asked Questions

ClinVar is used to look up the clinical significance of human genomic variants in relation to diseases and drug responses. It is widely used by clinical geneticists, researchers, and bioinformaticians to support variant interpretation, genomic medicine, and research.

Yes, ClinVar is completely free and publicly accessible. It is funded by the U.S. National Institutes of Health (NIH) and maintained by NCBI.

ClinVar offers a RESTful API for programmatic access as well as FTP bulk data downloads. Developers and bioinformaticians can use these to integrate ClinVar data into custom pipelines and applications.

ClinVar accepts submissions from clinical testing labs, research labs, genetics clinics, patient registries, locus-specific databases, expert panels, and organizations establishing practice guidelines. Registration is required through the ClinVar Submission Portal.

A VCV (Variant-Centric) record aggregates all submissions for a specific genomic variant regardless of condition, while an RCV (Variant-Condition) record organizes submissions by a specific variant-condition pair, allowing users to see classification in the context of a particular disease.