ClinVar: updates to support classifications of both germline and somatic variants
Open accessAbstract
ClinVar (www.ncbi.nlm.nih.gov/clinvar/) is a free, public database of human genetic variants and their relationships to disease, with >3 million variants submitted by >2800 organizations across the world. The database was recently updated to have three types of classifications: germline, oncogenicity and clinical impact for somatic variants. As for germline variants, classifications for somatic variants can be submitted in batches in a file submission or through the submission API; variants can also be submitted and updated one at a time in online submission forms. The ClinVar XML files were redesigned to allow multiple classification types. Both old and new formats of the XML are supported through the end of 2024. Data for somatic classifications were also added to the ClinVar VCF files and to several tab-delimited files. The ClinVar VCV pages were updated to display the three types of classifications, both as it was submitted and as it was aggregated by ClinVar. Clinical testing laboratories and others in the cancer community are invited to share their classifications of somatic variant classifications through ClinVar to provide transparency in genomic testing and improve patient care.
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Documented VUS have rapidly outstripped pathogenic variants in widely used clinical genomic databases such as ClinVar and now pose a major challenge in genetic diagnosis.
“Documented VUS have rapidly outstripped pathogenic variants in widely used clinical genomic databases such as ClinVar (Fig. 1) and now pose a major challenge in genetic diagnosis (24).”
From Massively parallel functional genomic assays in endocrinology: from promise to delivery (2026) · cites this paper as [24]
The Introduction identifies ClinVar as a routinely used clinical variant database with more than 3 million variants. But neither the Introduction nor the passages found by searching for VUS and uncertain significance compare VUS counts or growth with pathogenic variants, or state that VUS pose a major challenge in genetic diagnosis. (LLM, conf=0.78)
Experimental — accuracy not yet measuredThese standards ensure capture of essential details of experimental design to ensure reproducibility and integration with other resources such as ClinVar and gnomAD.
“These standards ensure capture of essential details of experimental design to ensure reproducibility and integration with other resources such as ClinVar (24) and gnomAD (103).”
From Massively parallel functional genomic assays in endocrinology: from promise to delivery (2026) · cites this paper as [24]
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Richards, S., Aziz, N., Bale, S., Bick, D., Das, S., Gastier-Foster, J., Grody, W. W., Hegde, M., Lyon, E., Spector, E., et al. (2015) · Genetics in Medicine · doi:10.1038/gim.2015.30 · Cited by 32,594 · see citing works
The current state of molecular testing in the treatment of patients with solid tumors, 2019
El‐Deiry, W. S., Goldberg, R. M., Lenz, H., Shields, A. F., Gibney, G. T., Tan, A. R., Brown, J., Eisenberg, B., Heath, E. I., Phuphanich, S., et al. (2019) · CA: A Cancer Journal for Clinicians · doi:10.3322/caac.21560 · Cited by 264 · see citing works
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Massively parallel functional genomic assays in endocrinology: from promise to delivery
Xu, J., Aslanzadeh, V., Kudla, G., & Semple, R. K. (2026) · Journal of Molecular Endocrinology · doi:10.1530/jme-25-0134
- Authors
- Landrum, M. J., Chitipiralla, S., Kaur, K., Brown, G., Chen, C., Hart, J., Hoffman, D., Jang, W., Liu, C., Maddipatla, Z., Maiti, R., Mitchell, J., Rezaie, T., Riley, G., Song, G., Yang, J., Ziyabari, L., Russette, A., & Kattman, B. L.
- Affiliations
- National Institutes of Health (US)
- Corresponding author
- Landrum, Melissa J
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2024-11-23
- Volume
- 53
- Issue
- D1
- Pages
- D1313-D1321
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC11701624
- OpenAlex
- W4404641556
- Cited by
- 182
- References
- 2
- Citations by year
- 2026: 119 · 2025: 62 · 2024: 1
- FWCI
- 44.71
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- public-domain
- Locations
- Nucleic Acids Research (publishedVersion, public-domain)
- PubMed Central (publishedVersion, public-domain)
- PubMed (publishedVersion)
- Funders
- National Library of Medicine
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer Genomics and Diagnostics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › BRCA gene mutations in cancer
- Keywords
- ClinVar, somatic mutations, germline mutations, variant interpretation, oncogenicity, clinical impact, VCF files, cancer genomics
- MeSH terms
- Humans, Neoplasms, Software, Genetic Variation, Genome, Human, Germ-Line Mutation, Genomics, Databases, Genetic
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