ClinVar: public archive of interpretations of clinically relevant variants
Open accessAbstract
ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/) at the National Center for Biotechnology Information (NCBI) is a freely available archive for interpretations of clinical significance of variants for reported conditions. The database includes germline and somatic variants of any size, type or genomic location. Interpretations are submitted by clinical testing laboratories, research laboratories, locus-specific databases, OMIM®, GeneReviews™, UniProt, expert panels and practice guidelines. In NCBI's Variation submission portal, submitters upload batch submissions or use the Submission Wizard for single submissions. Each submitted interpretation is assigned an accession number prefixed with SCV. ClinVar staff review validation reports with data types such as HGVS (Human Genome Variation Society) expressions; however, clinical significance is reported directly from submitters. Interpretations are aggregated by variant-condition combination and assigned an accession number prefixed with RCV. Clinical significance is calculated for the aggregate record, indicating consensus or conflict in the submitted interpretations. ClinVar uses data standards, such as HGVS nomenclature for variants and MedGen identifiers for conditions. The data are available on the web as variant-specific views; the entire data set can be downloaded via ftp. Programmatic access for ClinVar records is available through NCBI's E-utilities. Future development includes providing a variant-centric XML archive and a web page for details of SCV submissions.
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The individual gene estimates are concordant with the absence of any de novo mutations in NIPA1, NIPA2, CYFIP1, and TUBGCP5 in ClinVar.
“Our individual gene estimates are, however, concordant with the absence of any de novo mutations in NIPA1, NIPA2, CYFIP1 and TUBGCP5 in the public archive of interpretations of clinically relevant variants, ClinVar accessed March 2018 (http://www.ncbi.nlm.nih.gov/clinvar).47”
From Estimating the effect size of the 15Q11.2 BP1–BP2 deletion and its contribution to neurodevelopmental symptoms: recommendations for practice (2019) · cites this paper as [47]
The Introduction identifies ClinVar as a public database of submitted variant interpretations, supporting the citation’s identification of the archive. The paper does not report whether de novo mutations in NIPA1, NIPA2, CYFIP1, or TUBGCP5 were absent from ClinVar in March 2018; searches for those genes and de novo mutations found no such passage. The citing authors’ individual gene estimates are their own finding, not a finding attributed to this source. (LLM, conf=0.86)
Experimental — accuracy not yet measuredSome variants designated with the 'increased risk' classification in DTC raw data or by a third-party interpretation service were classified as benign at Ambry Genetics as well as several other clinical laboratories.
“In addition, some variants designated with the “increased risk” classification in DTC raw data or by a third-party interpretation service were classified as benign at Ambry Genetics as well as several other clinical laboratories, and are noted to be common variants in publicly available population frequency databases.”
From False-positive results released by direct-to-consumer genetic tests highlight the importance of clinical confirmation testing for appropriate patient care (2018) · cites this paper as [21]
The Introduction and Maintenance sections describe ClinVar’s aggregation of laboratory interpretations and how it displays conflicts, but neither reports the claimed DTC classifications or benign assessments by Ambry Genetics and other laboratories. Searches for “Ambry,” “increased risk,” and “direct-to-consumer” found no passage addressing those variants. (LLM, conf=0.76)
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Laurent, J. M., Janizek, J. D., Ruzo, M., Hinks, M. M., Hammerling, M. J., Narayanan, S., Ponnapati, M., White, A. D., & Rodriques, S. G. (2024) · arXiv · doi:10.48550/arxiv.2407.10362 · Cited by 21 · see citing works
“Contained in the variant_from_sequence_task.json file, these questions test the ability of models to correctly process sequences and lookup benign vs pathogenic mutations according to ClinVar [26].”
BackgroundLi, C., Zhang, L., Zhuo, Z., Su, F., Li, H., Xu, S., Liu, Y., Zhang, Z., Xie, Y., Yu, X., et al. (2023) · Theranostics · doi:10.7150/thno.79362 · Cited by 10 · see citing works
Blokhina, A. V., Ershova, A. I., Kiseleva, A. V., Sotnikova, E. A., Zharikova, A. A., Zaicenoka, M., Vyatkin, Y. V., Ramensky, V. E., Kutsenko, V. A., Garbuzova, E. V., et al. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms252312651 · Cited by 8 · see citing works
Autophagy dark genes: Can we find them with machine learning?
Ranjbar, M., Yang, J. J., Kumar, P., Byrd, D. R., Bearer, E. L., & Oprea, T. I. (2023) · Natural Sciences · doi:10.1002/ntls.20220067 · Cited by 7 · see citing works
InpherNet accelerates monogenic disease diagnosis using patients’ candidate genes’ neighbors
Yoo, B., Birgmeier, J., Bernstein, J. A., & Bejerano, G. (2021) · Genetics in Medicine · doi:10.1038/s41436-021-01238-2 · Cited by 4 · see citing works
- Authors
- Landrum, M. J., Lee, J. M., Benson, M., Brown, G., Chao, C., Chitipiralla, S., Gu, B., Hart, J., Hoffman, D., Hoover, J., Jang, W., Katz, K., Ovetsky, M., Riley, G., Sethi, A., Tully, R., Villamarin-Salomon, R., Rubinstein, W., & Maglott, D. R.
- Affiliations
- National Institutes of Health (US)
- Corresponding author
- Landrum, Melissa J.
- ORCID
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2015-11-17
- Volume
- 44
- Issue
- D1
- Pages
- D862-D868
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC4702865
- OpenAlex
- W2174602966
- Cited by
- 2,758
- References
- 16
- Citations by year
- 2026: 179 · 2025: 241 · 2024: 238 · 2023: 242 · 2022: 252 · 2021: 271 · 2020: 289 · 2019: 328 · 2018: 352 · 2017: 265 · 2016: 94 · 2014: 1
- FWCI
- 163.59
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- public-domain
- Locations
- Nucleic Acids Research (publishedVersion, public-domain)
- Europe PMC (PubMed Central) (publishedVersion, public-domain)
- PubMed Central (publishedVersion, public-domain)
- PubMed (publishedVersion)
- HighWire Press Open Archive (submittedVersion)
- Funders
- National Institutes of Health
- U.S. National Library of Medicine
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- ClinVar, variant interpretation, clinical significance, germline mutations, somatic mutations, variant nomenclature, HGVS, data standards
- MeSH terms
- Disease, Genes, Humans, Genetic Variation, Genome, Human, Databases, Genetic
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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