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ClinVar: improving access to variant interpretations and supporting evidence
2017
Nucleic Acids Research
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ClinVar continues to make improvements to its search and retrieval functions. ...
Data aggregated by variant are accessible on the website, in an improved set of variant call format files and as a new comprehensive XML report. ...
ACKNOWLEDGEMENTS We thank our partners in the ClinGen group, most notably Heidi Rehm, Christa Martin, Steven Harrison, Erin Riggs and Danielle Azzariti, for their continued feedback and guidance to make ...
doi:10.1093/nar/gkx1153
pmid:29165669
pmcid:PMC5753237
fatcat:ngbthvyavvejjdkin52xwrjmua
ClinVar: improvements to accessing data
2019
Nucleic Acids Research
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The ClinVar website and E-utilities both have been updated to support the VCV (variation in ClinVar) accession numbers found in the variant-centric XML file. ...
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 ...
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
ClinVar: public archive of interpretations of clinically relevant variants
2015
Nucleic Acids Research
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Interpretations are aggregated by variantcondition combination and assigned an accession number prefixed with RCV. ...
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. ...
ACKNOWLEDGEMENTS We thank our partners in the ClinGen group, most notably Heidi Rehm, Christa Martin, Steven Harrison, Erin Riggs and Danielle Metterville, for their continued feedback and guidance to ...
doi:10.1093/nar/gkv1222
pmid:26582918
pmcid:PMC4702865
fatcat:x4b6xdfj65ebtnpinz3m2mcm6u
Simple ClinVar: an interactive web server to explore and retrieve gene and disease variants aggregated in ClinVar database
2019
Nucleic Acids Research
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Our website will follow ClinVar monthly releases and provide easy access to ClinVar resources to a broader audience including basic and clinical scientists. ...
Here, we present Simple ClinVar (http://simple-clinvar.broadinstitute.org/) a web server application that is able to provide variant, gene and disease level summary statistics based on the entire ClinVar ...
ACKNOWLEDGEMENTS We thank the researchers and clinicians involved in the generation of clinical data contained in ClinVar. ...
doi:10.1093/nar/gkz411
pmid:31114901
pmcid:PMC6602488
fatcat:lsac4eplingtvnqvkle2isnr4q
ClinVar database of global familial hypercholesterolemia-associated DNA variants
2018
Human Mutation
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Collaborating to provide thorough, reliable evidence-based variant interpretation will ultimately improve the care of FH patients. ...
To further reform interpretation of FH-associated variants, areas for improvement in variant submissions were identified and addressed; these include a need for more detailed submissions and submission ...
TF was supported by the Ministry of Health of the Czech Republic, Grants nr. 16-29084A and 15-28277A (all rights reserved). ...
doi:10.1002/humu.23634
pmid:30311388
pmcid:PMC6206854
fatcat:voevcng4sjepzmqpbkqy4c2v4i
Clinotator: analyzing ClinVar variation reports to prioritize reclassification efforts
2018
F1000Research
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of the evidence supporting the variant clinical significance. ...
With the rapidly growing body of variant evidence, most submitters and researchers have limited resources to devote to variant curation. ...
We would also like to thank Mr. Alex Henrie, Ms. Sarah Hemphill, Dr. Karen Eilbeck and Dr. 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
ClinVar: public archive of relationships among sequence variation and human phenotype
2013
Nucleic Acids Research
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ClinVar accessions submissions reporting human variation, interpretations of the relationship of that variation to human health and the evidence supporting each interpretation. ...
accession of the format RCV000000000.0 and reports if there are conflicting clinical interpretations. ...
, interpretation of functional and clinical significance, methodology used to capture variant calls and supporting evidence. ...
doi:10.1093/nar/gkt1113
pmid:24234437
pmcid:PMC3965032
fatcat:ons2vfjgnfdr3hjadgnu6rki7a
Clinotator: analyzing ClinVar variation reports to prioritize reclassification efforts
2018
F1000Research
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of the evidence supporting the variant clinical significance. ...
With the rapidly growing body of variant evidence, most submitters and researchers have limited resources to devote to variant curation. ...
We would also like to thank Mr. Alex Henrie, Ms. Sarah Hemphill, Dr. Karen Eilbeck and Dr. Heidi Rehm for advanced access to their upcoming publication on the ClinVar Miner software and web utility. ...
doi:10.12688/f1000research.14470.2
fatcat:vtjkbqifxnemjfxslhhynxdjiq
Reinterpretation of common pathogenic variants in ClinVar revealed a high proportion of downgrades
2020
Scientific Reports
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This study aimed to interpret and reclassify common pathogenic (P) and likely pathogenic (LP) variants in ClinVar and to identify indicators linked with reclassification. ...
ClinVar provides a universal platform for users who intend to share the classification variants, resulting in the improved concordance of variant interpretation. ...
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
Sources of discordance among germ-line variant classifications in ClinVar
2017
Genetics in Medicine
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Ongoing improvements to ClinVar may make it easier to use, particularly for nonexpert users. ...
ClinVar can be a reliable resource supporting variant interpretation, quality assessment, and clinical practice when factors uncovered in this study are taken into account. ...
ACKNOWLEDGMENTS We are deeply grateful to the laboratories and other groups who are working to advance medical care by submitting data to the ClinVar database. ...
doi:10.1038/gim.2017.60
pmid:28569743
pmcid:PMC5632819
fatcat:ubzwwe4s25fjhak5ytp2s7orhi
Clinical laboratories collaborate to resolve differences in variant interpretations submitted to ClinVar
2017
Genetics in Medicine
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identify the basis of interpretation differences and to investigate if data sharing and reassessment resolves interpretation differences by analyzing a subset of variants. ...
Purpose-Data sharing through ClinVar offers a unique opportunity to identify interpretation differences between laboratories. ...
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
Variability in gene-based knowledge impacts variant classification: an analysis of FBN1 missense variants in ClinVar
2019
European Journal of Human Genetics
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In order to assess variability in classification of FBN1 variants, 674 FBN1 missense variants from 18 ClinVar submitters were compared and reanalyzed using FBN1-specific criteria and ACMG/AMP 2015 guidelines ...
Non-cysteine critical residue variants were less likely to be classified as (L)P [55.3% (78/141)] than cysteine variants [91.3% (283/310)] and were more likely to lack evidence citing the functional significance ...
as ClinVar, an NIH open-access database of clinically observed variants and their classifications. ...
doi:10.1038/s41431-019-0440-3
pmid:31227806
pmcid:PMC6777626
fatcat:a6ayra4qjvaqjk7rgy3esqekqe
An enhanced workflow for variant interpretation in UniProtKB/Swiss-Prot improves consistency and reuse in ClinVar
2019
Database: The Journal of Biological Databases and Curation
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We show that existing interpretations of variant pathogenicity in UniProtKB/Swiss-Prot and ClinVar are highly concordant, with 88% of variants that are common to the two resources having interpretations ...
We have now incorporated ACMG guidelines and ClinGen tools into the UniProt Knowledgebase (UniProtKB) curation workflow and routinely submit variant data from UniProtKB/Swiss-Prot to ClinVar. ...
Acknowledgements We are grateful to the development team of the ClinGen pathogenicity calculator for generating the files for submission to ClinVar. Conflict of interest. None declared. ...
doi:10.1093/database/baz040
pmid:30937429
pmcid:PMC6444058
fatcat:oel3w3qdszeuxc3b5ldpwfxrbe
Points to consider for sharing variant-level information from clinical genetic testing with ClinVar
2018
Molecular Case Studies
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We propose specific data elements from interpreted genomic variants that are appropriate for submission to ClinVar when direct patient consent was not sought and describe situations in which obtaining ...
ClinGen has collaborated with ClinVar and the National Human Genome Research Institute to develop points to consider for clinical laboratories on sharing de-identified variant-level data in light of both ...
Acknowledgments We thank the many ClinVar submitters for sharing their data as well as Elyse Galloway and Kate Saylor, formerly of the NHGRI Division of Policy, Communications, and Education. ...
doi:10.1101/mcs.a002345
pmid:29437798
pmcid:PMC5793773
fatcat:4pewasfjmzbs3cec3y2g7l7sea
In-silico Analysis of NF1 Missense Variants in ClinVar: Translating Variant Predictions into Variant Interpretation and Classification
2020
International Journal of Molecular Sciences
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Methods: Here, we analyzed three different computational methods, VEST3, REVEL and ClinPred, and after extracting predictions scores for 1585 NF1 missense variants listed in ClinVar, evaluated their performances ...
With the advent of next-generation sequencing in genetic testing, predicting the pathogenicity of missense variants represents a major challenge potentially leading to misdiagnoses in the clinical setting ...
Conclusions The focus of our study was to improve NF1 missense variants interpretation and classification, considering that 66.2% (1045/1579) of missense variants listed at ClinVar were reported by single ...
doi:10.3390/ijms21030721
pmid:31979111
pmcid:PMC7037781
fatcat:5nwqyygxzrgg5ohwydjc3fhieq
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