ClinVar Miner

Variants from Baylor-Hopkins Center for Mendelian Genomics, Johns Hopkins University School of Medicine with conflicting interpretations

Location: United States  Primary collection method: research
Minimum review status of the submission from Baylor-Hopkins Center for Mendelian Genomics, Johns Hopkins University School of Medicine: Collection method of the submission from Baylor-Hopkins Center for Mendelian Genomics, Johns Hopkins University School of Medicine:
Minimum review status of the other submission: Collection method of the other submission:
Minimum conflict level:
ClinVar version:

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
118 49 0 18 5 2 6 31

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
Baylor-Hopkins Center for Mendelian Genomics, Johns Hopkins University School of Medicine pathogenic likely pathogenic uncertain significance likely benign benign affects risk factor
pathogenic 0 11 3 0 0 0 0
likely pathogenic 7 0 1 0 0 1 1
uncertain significance 2 1 0 3 3 0 0

Submitter to submitter summary #

Total submitters: 29
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
OMIM 0 44 0 2 0 1 2 5
Invitae 0 14 0 0 4 0 1 5
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute 0 1 0 3 0 0 0 3
Centre for Mendelian Genomics, University Medical Centre Ljubljana 0 0 0 3 0 0 0 3
3billion 0 2 0 2 0 0 1 3
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories 0 0 0 1 1 0 0 2
Revvity Omics, Revvity 0 3 0 1 0 0 1 2
Fulgent Genetics, Fulgent Genetics 0 3 0 2 0 0 0 2
Genetic Services Laboratory, University of Chicago 0 1 0 1 0 0 0 1
PreventionGenetics, part of Exact Sciences 0 0 0 1 0 0 0 1
MGZ Medical Genetics Center 0 0 0 1 0 0 0 1
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 0 3 0 1 0 0 0 1
Mendelics 0 1 0 0 1 0 0 1
Genomic Research Center, Shahid Beheshti University of Medical Sciences 0 1 0 0 0 0 1 1
Illumina Laboratory Services, Illumina 0 2 0 0 1 0 0 1
Shaikh Laboratory, University of Colorado 0 0 0 1 0 0 0 1
Center for Medical Genetics Ghent, University of Ghent 0 0 0 0 0 0 1 1
Hadassah Hebrew University Medical Center 0 0 0 1 0 0 0 1
Garry R Cutting Laboratory, Johns Hopkins University 0 0 0 0 0 0 1 1
Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India 0 0 0 1 0 0 0 1
Genetics and Molecular Pathology, SA Pathology 0 1 0 1 0 0 0 1
SIB Swiss Institute of Bioinformatics 0 0 0 1 0 0 0 1
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen 0 0 0 0 1 0 0 1
UNC Molecular Genetics Laboratory, University of North Carolina at Chapel Hill 0 0 0 1 0 0 0 1
National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center 0 0 0 0 0 1 0 1
Centre for Human Genetics, University of Kinshasa 0 0 0 1 0 0 0 1
Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center 0 1 0 1 0 0 0 1
DASA 0 0 0 1 0 0 0 1
Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein 0 0 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 31
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_001134363.3(RBM20):c.2662G>A (p.Asp888Asn) rs201370621 0.00344
NM_001370466.1(NOD2):c.850C>T (p.Arg284Trp) rs104895427 0.00051
NM_002887.4(RARS1):c.1367C>T (p.Ser456Leu) rs139644798 0.00044
NM_001218.5(CA12):c.908-1G>A rs148438059 0.00043
NM_145064.3(STAC3):c.851G>C (p.Trp284Ser) rs140291094 0.00039
NM_152415.3(VPS37A):c.700C>A (p.Leu234Ile) rs150912414 0.00029
NM_016111.4(TELO2):c.1100G>T (p.Cys367Phe) rs202020308 0.00016
NM_001982.4(ERBB3):c.4009G>A (p.Ala1337Thr) rs755855285 0.00014
NM_016111.4(TELO2):c.2296G>A (p.Val766Met) rs371675497 0.00010
NM_000275.3(OCA2):c.2360C>T (p.Ala787Val) rs200457227 0.00004
NM_002296.4(LBR):c.1640A>G (p.Asn547Ser) rs374343844 0.00004
NM_057176.3(BSND):c.35T>C (p.Ile12Thr) rs121908144 0.00002
NM_003482.4(KMT2D):c.185C>T (p.Pro62Leu) rs371342351 0.00001
NM_005896.4(IDH1):c.395G>A (p.Arg132His) rs121913500 0.00001
NM_017780.4(CHD7):c.5131G>A (p.Asp1711Asn) rs748590759 0.00001
NM_000138.5(FBN1):c.7003C>T (p.Arg2335Trp) rs794728262
NM_000441.2(SLC26A4):c.269C>T (p.Ser90Leu) rs370588279
NM_001312673.2(PCYT1A):c.990del (p.Ser331fs) rs587777193
NM_001614.5(ACTG1):c.721G>A (p.Glu241Lys) rs267606631
NM_003036.4(SKI):c.100G>A (p.Gly34Ser) rs387907306
NM_003036.4(SKI):c.347G>A (p.Gly116Glu) rs387907303
NM_003238.6(TGFB2):c.294_308del (p.Ala100_Tyr104del) rs398122883
NM_003238.6(TGFB2):c.904C>T (p.Arg302Cys) rs869312903
NM_003482.4(KMT2D):c.11568GCA[6] (p.Gln3863dup) rs748986705
NM_003482.4(KMT2D):c.12268C>T (p.Gln4090Ter) rs1555188155
NM_003482.4(KMT2D):c.1329_1332del (p.Pro444fs) rs587783689
NM_003482.4(KMT2D):c.5124_5125del (p.Arg1709fs) rs886043506
NM_003482.4(KMT2D):c.6595del (p.Tyr2199fs) rs398123753
NM_004004.6(GJB2):c.428G>A (p.Arg143Gln) rs104894401
NM_004782.4(SNAP29):c.223del (p.Val75fs) rs869312906
NM_031263.4(HNRNPK):c.257G>A (p.Arg86His) rs863223403

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