ClinVar Miner

Variants from Genomics And Bioinformatics Analysis Resource, Columbia University with conflicting interpretations

Location: United States  Primary collection method: research
Minimum review status of the submission from Genomics And Bioinformatics Analysis Resource, Columbia University: Collection method of the submission from Genomics And Bioinformatics Analysis Resource, Columbia University:
Minimum review status of the other submission: Collection method of the other submission:
Minimum conflict level:

If a variant has more than two submissions, it may have multiple conflicts and therefore be counted in more than one conflict column. If this is the case, the "Variants with any kind of conflict" cell will be less than the sum of the conflicted variants cells to its left.

Variants with only 1 submission per condition Variants with at least 2 submissions on the same condition and no conflicts Variants with a synonymous conflict
(e.g. benign vs non-pathogenic)
Variants with a confidence conflict
(e.g. benign vs likely benign)
Variants with a benign or likely benign vs uncertain conflict Variants with a category conflict
(e.g. benign vs affects)
Variants with a clinically significant conflict
(e.g. benign vs pathogenic)
Variants with any conflict
30 28 2 28 0 0 6 32

Significance breakdown #

In the table below, cells that correspond to a term paired with itself represent synonymous conflicts, i.e. variants that have been annotated with different terms that map to the same standard term. To compare the terms that were actually submitted, check the box in the filters section at the top of this page.

All submitters
Genomics And Bioinformatics Analysis Resource, Columbia University pathogenic likely pathogenic uncertain significance benign
pathogenic 2 15 2 1
likely pathogenic 13 0 3 0

Submitter to submitter summary #

Total submitters: 33
Download table as spreadsheet
Submitter Variants with only 1 submission per condition Variants with at least 2 submissions on the same condition and no conflicts Variants with a synonymous conflict
(e.g. benign vs non-pathogenic)
Variants with a confidence conflict
(e.g. benign vs likely benign)
Variants with a benign or likely benign vs uncertain conflict Variants with a category conflict
(e.g. benign vs affects)
Variants with a clinically significant conflict
(e.g. benign vs pathogenic)
Variants with any conflict
Labcorp Genetics (formerly Invitae), Labcorp 0 19 2 6 0 0 0 8
Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre 0 3 0 3 0 0 2 5
Counsyl 0 3 0 3 0 0 1 4
Fulgent Genetics, Fulgent Genetics 0 18 0 3 0 0 1 4
3billion 0 13 0 3 0 0 0 3
Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center 0 5 0 2 0 0 0 2
Illumina Laboratory Services, Illumina 0 7 0 1 0 0 1 2
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine 0 6 0 2 0 0 0 2
OMIM 0 14 0 1 0 0 1 2
University of Washington Center for Mendelian Genomics, University of Washington 0 0 0 2 0 0 0 2
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute 0 9 0 2 0 0 0 2
CeGaT Center for Human Genetics Tuebingen 0 1 0 1 0 0 0 1
Clinical Genomics Laboratory, Washington University in St. Louis 0 3 0 0 0 0 1 1
Department of Pathology and Laboratory Medicine, Sinai Health System 0 3 0 0 0 0 1 1
Equipe Genetique des Anomalies du Developpement, Université de Bourgogne 0 4 0 1 0 0 0 1
Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics 0 1 0 0 0 0 1 1
Geisinger Clinic, Geisinger Health System 0 0 0 1 0 0 0 1
GeneDx 0 2 0 1 0 0 0 1
Genomic Medicine Lab, University of California San Francisco 0 2 0 1 0 0 0 1
Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine 0 2 0 1 0 0 0 1
Immunogenetics and Transplant Biology Service, University Hospital "Città della Salute e della Scienza di Torino" 0 3 0 1 0 0 0 1
Institute of Human Genetics, University of Leipzig Medical Center 0 7 0 1 0 0 0 1
Johns Hopkins Genomics, Johns Hopkins University 0 3 0 0 0 0 1 1
Laboratory of Medical Genetics, National & Kapodistrian University of Athens 0 6 0 1 0 0 0 1
Mendelics 0 9 0 1 0 0 0 1
Molecular Biology Laboratory, Fundació Puigvert 0 0 0 1 0 0 0 1
Molecular Genetics Lab, CHRU Brest 0 0 0 1 0 0 0 1
Myriad Genetics, Inc. 0 10 0 1 0 0 0 1
Natera, Inc. 0 12 0 1 0 0 0 1
PreventionGenetics, part of Exact Sciences 0 0 0 1 0 0 0 1
Revvity Omics, Revvity 0 6 0 1 0 0 0 1
Variantyx, Inc. 0 3 0 1 0 0 0 1
deCODE genetics, Amgen 0 1 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 32
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_000410.4(HFE):c.187C>G (p.His63Asp) rs1799945 0.10170
NM_000410.4(HFE):c.845G>A (p.Cys282Tyr) rs1800562 0.03738
NM_001127701.1(SERPINA1):c.1096G>A (p.Glu366Lys) rs28929474 0.01282
NM_000443.4(ABCB4):c.2800G>A (p.Ala934Thr) rs61730509 0.00389
NM_000243.3(MEFV):c.2177T>C (p.Val726Ala) rs28940579 0.00147
NM_138694.4(PKHD1):c.12027C>G (p.Tyr4009Ter) rs143616240 0.00098
NM_000492.4(CFTR):c.3909C>G (p.Asn1303Lys) rs80034486 0.00016
NM_024753.5(TTC21B):c.626C>T (p.Pro209Leu) rs140511594 0.00011
NM_000243.3(MEFV):c.2082G>A (p.Met694Ile) rs28940578 0.00007
NM_003742.4(ABCB11):c.1708G>A (p.Ala570Thr) rs886043807 0.00003
NM_138694.4(PKHD1):c.1123C>T (p.Arg375Trp) rs376040501 0.00003
NM_002074.5(GNB1):c.229G>A (p.Gly77Ser) rs758432471 0.00001
NM_002074.5(GNB1):c.239T>A (p.Ile80Asn) rs752746786 0.00001
NM_003742.4(ABCB11):c.403G>A (p.Glu135Lys) rs752992432 0.00001
NM_007214.5(SEC63):c.292C>T (p.Arg98Ter) rs768568123 0.00001
NM_175914.5(HNF4A):c.1198C>T (p.Arg400Ter) rs1413742263 0.00001
NM_000020.3(ACVRL1):c.889del (p.His297fs) rs1060503245
NM_000038.6(APC):c.3340C>T (p.Arg1114Ter) rs121913331
NM_000038.6(APC):c.4174del (p.Ser1392fs) rs1765620003
NM_000053.4(ATP7B):c.2447+1G>T rs1958431105
NM_000053.4(ATP7B):c.524_525del (p.Lys175fs) rs558037268
NM_000053.4(ATP7B):c.778dup (p.Gln260fs) rs786204570
NM_000214.3(JAG1):c.1395+3A>G rs886044220
NM_000292.3(PHKA2):c.3210_3212del (p.Arg1072del) rs1555989523
NM_000492.3(CFTR):c.1521_1523del (p.Phe508del) rs113993960
NM_000492.4(CFTR):c.1A>G (p.Met1Val) rs397508328
NM_001009944.3(PKD1):c.6813_6814del (p.Arg2272fs) rs1567191145
NM_001065.4(TNFRSF1A):c.123T>G (p.Asp41Glu) rs104895271
NM_001244008.2(KIF1A):c.914C>T (p.Pro305Leu) rs1131690804
NM_002465.4(MYBPC1):c.788T>G (p.Leu263Arg) rs1565943228
NM_002633.3(PGM1):c.1378_1379del (p.Ala461fs) rs763428801
NM_003742.4(ABCB11):c.1409G>A (p.Arg470Gln) rs1463057954

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