ClinVar is proud to announce the submission of the one millionth record to its database.

The millionth submission was published on Friday, December 20, 2019, a milestone achievement for providing open access to human variant data with asserted consequence to the clinical genetics and research communities.

ClinVar extends its thanks to the many laboratories, partners, and members of the community whose efforts and adoption of the practice of data-sharing paved the way for this achievement. All organizations that contributed to ClinVar’s genetics resources share in this accomplishment, with special recognition reserved for ClinGen and several of their members, including EGL Genetic Diagnostics/Eurofins Clinical Diagnostics, GeneDx, Invitae, and Laboratory for Molecular Medicine/Partners HealthCare Personalized Medicine, whose early submissions helped jump-start ClinVar’s database.

Each submission has represented a step towards progress for the community and patients alike. Since ClinVar’s inception in 2013, ClinVar has garnered over 568,000 unique variants from these one million submissions. Expert panels have improved data quality and assertions of clinical significance for records by providing expert-curated interpretations of variants. The first expert panel to share interpretations was the International Society for Gastrointestinal Hereditary Tumours (InSiGHT) in 2013, followed by CFTR2, ENIGMA, and PharmGKB. With the addition of 7 more expert panels, all developed by ClinGen, ClinVar now has 11 expert panels that have provided more than 10,000 expert-curated variants. This database, being made freely accessible and with valuable, crowdsourced clinical context to the data, has become an irreplaceable part of the workflow of genetics researchers and clinical genetics testing laboratories, whose work impacts countless lives.

One such example from 2018 of how ClinVar improves patient outcomes begins with two laboratories independently researching the same variant. Each laboratory interpreted the variant as a variant of uncertain significance (VUS) and submitted this data to ClinVar.

When one of the laboratories was contacted by a concerned pregnant patient whose fetus harbored the variant, ClinVar enabled the laboratories to exchange case-level findings and conclude that the variant was Likely Benign, allowing the variant to be reclassified. Because of the reclassification aided by ClinVar, the family’s worry and stress were relieved.

Over the past six years, ClinVar has grown into a broad, international resource, receiving submissions from more than 1,300 organizations from 73 countries. Every month, ClinVar receives and processes an average of 13,600 submitted records, representing an average of 9,200 distinct variants. These submissions come primarily from organizations performing clinical testing, with the remainder coming from organizations performing research, and other sources, including locus-specific databases (LSDBs), expert panels, and resources such as OMIM®, GeneReviews®, and UniProt. ClinVar also invites clinicians and patient registries to submit phenotypic data for patients who have had genetic testing, since clinical testing laboratories rarely receive this information.

As part of ClinVar’s commitment to open data, the ClinVar team strives to ensure this data is made accessible in a timely fashion while maintaining the highest levels of accuracy and data quality. Your continued support and submission of records to the database is appreciated. ClinVar will continue to make enhancements that improve how genetic variant data is represented for researchers and clinicians, and we invite you to provide any feedback you may have by contacting us.

We at ClinVar are proud to have reached this milestone—not just for how many records have been submitted, but for the improved patient outcomes and advancement to genetics research this number represents. To our partners and to the clinical genetics community, we thank you for your support in this achievement.

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