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ClinVar: public archive of interpretations of clinically relevant variants
2015
Nucleic Acids Research
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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 ...
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. ...
useful for the clinical genetics community. ...
doi:10.1093/nar/gkv1222
pmid:26582918
pmcid:PMC4702865
fatcat:x4b6xdfj65ebtnpinz3m2mcm6u
ClinVar data parsing
2017
Wellcome Open Research
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.: Using high-resolution variant frequencies to empower clinical genome interpretation. Genet Med. 2017. PubMed Abstract | Publisher Full Text ...
Additionally, the tables are augmented with allele frequencies from the ExAC and gnomAD datasets as these are often consulted when analyzing ClinVar variants. ...
Software availability The pipeline, its fully parsed data files and example data files are available: https://github.com/macarthur-lab/clinvar Archived source code as at the time of publication: https: ...
doi:10.12688/wellcomeopenres.11640.1
pmid:28630944
pmcid:PMC5473414
fatcat:ahkz2duzebdtnoeaksockxplc4
ClinVar: improvements to accessing data
2019
Nucleic Acids Research
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ClinVar is a freely available, public archive of human genetic variants and interpretations of their relationships to diseases and other conditions, maintained at the National Institutes of Health (NIH ...
Submitted interpretations of variants are aggregated and made available on the ClinVar website (https://www.ncbi.nlm.nih.gov/clinvar/), and as downloadable files via FTP and through programmatic tools ...
ACKNOWLEDGEMENTS The authors thank the ClinVar users who have participated in user experience interviews. We welcome feedback from the community. ...
doi:10.1093/nar/gkz972
pmid:31777943
pmcid:PMC6943040
fatcat:iwsisqgnovh3lc4c5z22v3l3oi
Reinterpretation of common pathogenic variants in ClinVar revealed a high proportion of downgrades
2020
Scientific Reports
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ClinVar provides a universal platform for users who intend to share the classification variants, resulting in the improved concordance of variant interpretation. ...
Most of the reclassifications were of variants with a low rank, an older classification, a higher allele frequency, or which were collected through methods other than clinical testing. ...
The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. ...
doi:10.1038/s41598-019-57335-5
pmid:31942019
pmcid:PMC6962394
fatcat:dxvdhc7as5b2bnzdg5uzf45bcy
Clinotator: analyzing ClinVar variation reports to prioritize reclassification efforts
2018
F1000Research
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While ClinVar has become an indispensable resource for clinical variant interpretation, its sophisticated structure provides it with a daunting learning curve. ...
of the evidence supporting the variant clinical significance. ...
Heidi Rehm for advanced access to their upcoming publication on the ClinVar Miner software and web utility. ...
doi:10.12688/f1000research.14470.1
pmid:29862020
pmcid:PMC5941247
fatcat:63wndzm6dfasddokzuv3s6pexa
Clinical laboratories collaborate to resolve differences in variant interpretations submitted to ClinVar
2017
Genetics in Medicine
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Methods-ClinVar variants with submissions from at least two of the four participating laboratories were compared. ...
identify the basis of interpretation differences and to investigate if data sharing and reassessment resolves interpretation differences by analyzing a subset of variants. ...
We thank all ClinVar submitters for sharing their data and Jim Carver and Jessica Burgess for creating the figures. ...
doi:10.1038/gim.2017.14
pmid:28301460
pmcid:PMC5600649
fatcat:mhjrpwp7evhurhkikw7ct4tg44
tmVar 2.0: integrating genomic variant information from literature with dbSNP and ClinVar for precision medicine
2017
Bioinformatics
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Motivation: Despite significant efforts in expert curation, clinical relevance about most of the 154 million dbSNP reference variants (RS) remains unknown. ...
variants curated in ClinVar. ...
Funding This work was supported by the National Institutes of Health intramural research program, National Library of Medicine. Conflict of Interest: none declared. ...
doi:10.1093/bioinformatics/btx541
pmid:28968638
pmcid:PMC5860583
fatcat:ym74zidyt5dyvefjsrpusno57q
Scaling resolution of variant classification differences in ClinVar between 41 clinical laboratories through an outlier approach
2018
Human Mutation
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Outliers were identified by first comparing ClinVar submissions from 41 clinical laboratories to detect variants with medically significant differences between the laboratories (650 variants). ...
Next, medically significant differences were filtered for variants with ≥3 classifications (244 variants), of which 87.6% (213 variants) had a majority consensus in ClinVar, thus allowing for identification ...
Acknowledgments Research reported in this publication was supported in part by the National Human Genome Research Institute (NHGRI) under award U41HG006834. ...
doi:10.1002/humu.23643
pmid:30311378
pmcid:PMC6188667
fatcat:ihljhckrl5g3datno34pnwu5yu
Critical assessment of secondary findings in genes linked to primary arrhythmia syndromes
2020
Human Mutation
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Comparison of the databases ClinVar, LOVD and HGMD showed impactful differences (0.2% to 1.3%) in variant interpretation improvable by expert-curation depending on database and classification system used ...
Databases provide conflicting results for the purpose of identifying pathogenic variants in SF associated with IPAS at a level of sufficient evidence for clinical return. ...
public archive of interpretations of clinically relevant variants (ClinVar), Leiden Open-source Variant Database (LOVD), or by Medical Genetics Center (MGZ)-curators were listed DIEBOLD ET AL. | 1027 benign ...
doi:10.1002/humu.23996
pmid:32048431
fatcat:6kurx7l4rbdepl7a35ih7sahke
Providing Access to Genomic Variant Knowledge in a Healthcare Setting: A Vision for the ClinGen Electronic Health Records Workgroup
2015
Clinical Pharmacology and Therapeutics
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Acknowledgments The ClinGen Consortium is funded by The National Human Genome Research Institute (NHGRI), in conjunction with additional funding from The Eunice Kennedy Shriver National Institute of Child ...
ClinVar archives assertions of clinical significance for variants related to specific conditions, and thus, relies on voluntary submissions from clinical testing labs, researchers, locus-specific databases ...
clinically relevant variants" (www.clinicalgenome.org) [1] . ...
doi:10.1002/cpt.270
pmid:26418054
pmcid:PMC4724305
fatcat:bjy2m7rrcjecnnoyauuehpv5xi
ClinGen — The Clinical Genome Resource
2015
New England Journal of Medicine
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Five years later, during a routine clinic visit of one of the genotype-positive family members, the cardiologist queries a database for current knowledge on the genetic variant and discovers that the variant ...
The patient's family pursues genetic testing that shows a "likely pathogenic" variant for the condition on the basis of a study in an original research publication. ...
The first is ClinVar, which is a database at the National Center for Biotechnology Information that archives information submitted about variants with medical relevance. ...
doi:10.1056/nejmsr1406261
pmid:26014595
pmcid:PMC4474187
fatcat:sc5t4l5csnfodfpzmpfinr6zai
Comparison of Open-access Databases for Clinical Variant Interpretation in Cancer: A Case Study of MDS/AML
2021
Cancer Genomics & Proteomics
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Public databases provide decision support for interpreting variants but there is still need for manual curation. ...
We compared three meta-databases and 12 databases for a dataset of patients with myelodysplastic syndrome or acute myeloid leukemia. Clinical implications were found for 13% of all variants. ...
We are also grateful to Albina Caetano da Silva and Nicolette Banck for moral support and proof-reading of the article. ...
doi:10.21873/cgp.20250
pmid:33608312
pmcid:PMC7943210
fatcat:iofshvy3anheveotehixitehxa
Genetic variant interpretation: a primer for clinicians
2021
Internal medicine journal (Print)
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Understanding these advances in genetic variant interpretation may allow practising clinicians to develop a more nuanced appreciation of the role genetic variant interpretation can play in the diagnosis ...
In this article, we consider genetic variant interpretation with reference to efforts to better understand variation in the mismatch repair genes and their relation to Lynch syndrome - the most common ...
The keystone database for ClinGen is ClinVar, a free public archive of variants and corresponding interpretations. ...
doi:10.1111/imj.15485
pmid:34541770
fatcat:ufocrxckqvan5ogtp22646nrbu
DATA SHARING AND REPRODUCIBLE CLINICAL GENETIC TESTING: SUCCESSES AND CHALLENGES
2016
Biocomputing 2017
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Open sharing of clinical genetic data promises to both monitor and eventually improve the reproducibility of variant interpretation among clinical testing laboratories. ...
A significant public data resource has been developed by the NIH ClinVar initiative, which includes submissions from hundreds of laboratories and clinics worldwide. ...
Recently, the National Institutes of Health established ClinVar, "a freely available archive for interpretations of clinical significance of variants for reported conditions" [Landrum 2016 ]. ...
doi:10.1142/9789813207813_0017
pmid:27896972
pmcid:PMC5340191
fatcat:3pmowpgrtvgmfpjtgszqghzesu
Using Long-Term Follow-Up Data to Classify Genetic Variants in Newborn Screened Conditions
2022
Frontiers in Genetics
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We found 564 genetic variants with accompanying phenotypic data and identified that 161 of the 564 variants (29%) were not included in ClinVar. ...
This work demonstrates that secondary analysis of longitudinal data collected as part of NBS finds unreported genetic variants and the accompanying clinical information can inform the relationship between ...
ACKNOWLEDGMENTS The following individuals were members of the IBEMC: ...
doi:10.3389/fgene.2022.859837
pmid:35692825
pmcid:PMC9178101
fatcat:fguv76qxebb35n7pac2kbqzsp4
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