ClinVar Miner

Variants from Molecular Genetics Laboratory, BC Children's and BC Women's Hospitals with conflicting interpretations

Location: Canada  Primary collection method: clinical testing
Minimum review status of the submission from Molecular Genetics Laboratory, BC Children's and BC Women's Hospitals: Collection method of the submission from Molecular Genetics Laboratory, BC Children's and BC Women's Hospitals:
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
163 97 0 50 20 1 16 73

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
Molecular Genetics Laboratory, BC Children's and BC Women's Hospitals pathogenic likely pathogenic uncertain significance likely benign benign risk factor
pathogenic 0 19 3 0 0 0
likely pathogenic 15 0 7 1 0 0
uncertain significance 3 4 0 5 2 1
likely benign 0 0 13 0 14 0
benign 0 0 1 2 0 0

Submitter to submitter summary #

Total submitters: 53
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
Invitae 0 46 0 16 3 0 9 28
Illumina Laboratory Services, Illumina 0 13 0 5 10 0 0 15
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 0 13 0 3 3 0 1 7
Genome-Nilou Lab 0 14 0 2 2 0 1 5
OMIM 0 29 0 3 0 1 0 4
CFTR-France 0 1 0 3 0 0 1 4
GeneDx 0 12 0 2 0 0 1 3
Counsyl 0 5 0 2 0 0 1 3
Natera, Inc. 0 16 0 1 2 0 0 3
Baylor Genetics 0 17 0 2 0 0 0 2
Genome Diagnostics Laboratory, The Hospital for Sick Children 0 2 0 0 0 0 2 2
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories 0 4 0 2 0 0 0 2
Ambry Genetics 0 6 0 1 0 0 1 2
Revvity Omics, Revvity 0 10 0 1 0 0 1 2
PreventionGenetics, part of Exact Sciences 0 5 0 0 1 0 1 2
Eurofins Ntd Llc (ga) 0 6 0 0 0 0 2 2
Quest Diagnostics Nichols Institute San Juan Capistrano 0 3 0 1 0 0 1 2
Institute of Human Genetics, FAU Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg 0 2 0 2 0 0 0 2
CHU Sainte-Justine Research Center, University of Montreal 0 0 0 2 0 0 0 2
CeGaT Center for Human Genetics Tuebingen 0 8 0 0 0 0 2 2
Equipe Genetique des Anomalies du Developpement, Université de Bourgogne 0 1 0 2 0 0 0 2
Athena Diagnostics Inc 0 1 0 1 0 0 0 1
Center for Human Genetics, Inc, Center for Human Genetics, Inc 0 2 0 1 0 0 0 1
Clinical Molecular Genetics Laboratory, Johns Hopkins All Children's Hospital 0 1 0 1 0 0 0 1
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine 0 6 0 1 0 0 0 1
Mendelics 0 10 0 1 0 0 0 1
Mayo Clinic Laboratories, Mayo Clinic 0 2 0 0 0 0 1 1
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute 0 8 0 1 0 0 0 1
ClinVar Staff, National Center for Biotechnology Information (NCBI) 0 1 0 0 0 0 1 1
Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine 0 0 0 1 0 0 0 1
Institute Of Human Genetics Munich, Klinikum Rechts Der Isar, Tu München 0 8 0 1 0 0 0 1
Genomic Research Center, Shahid Beheshti University of Medical Sciences 0 1 0 0 0 0 1 1
Neurogenetics Laboratory, GH Pitie Salpetriere APHP 0 0 0 1 0 0 0 1
Centre de Biologie Pathologie Génétique, Centre Hospitalier Universitaire de Lille 0 0 0 1 0 0 0 1
Molecular Diagnostic Laboratory for Inherited Cardiovascular Disease, Montreal Heart Institute 0 0 0 0 1 0 0 1
U4M - Lille University & CHRU Lille, Université de Lille - CHRU de Lille 0 0 0 1 0 0 0 1
Institute of Human Genetics, University of Leipzig Medical Center 0 7 0 1 0 0 0 1
SIB Swiss Institute of Bioinformatics 0 2 0 1 0 0 0 1
Yale Center for Mendelian Genomics, Yale University 0 0 0 1 0 0 0 1
Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard 0 1 0 1 0 0 0 1
Johns Hopkins Genomics, Johns Hopkins University 0 1 0 1 0 0 0 1
Institute of Reproductive Genetics, University of Münster 0 0 0 0 0 0 1 1
INGEBI, INGEBI / CONICET 0 2 0 0 1 0 0 1
The ITHANET community portal, The Cyprus Institute of Neurology and Genetics 0 4 0 1 0 0 0 1
New York Genome Center 0 1 0 1 0 0 0 1
Pars Genome Lab 0 0 0 1 0 0 0 1
Molecular Genetics Lab, CHRU Brest 0 0 0 1 0 0 0 1
Pediatric Genetics Clinic, Sheba Medical Center 0 1 0 1 0 0 0 1
ClinGen Familial Hypercholesterolemia Variant Curation Expert Panel 0 0 0 0 0 0 1 1
Neuberg Supratech Reference Laboratories Pvt Ltd, Neuberg Centre for Genomic Medicine 0 3 0 1 0 0 0 1
Genomics England Pilot Project, Genomics England 0 1 0 1 0 0 0 1
Division Of Personalized Genomic Medicine, Columbia University Irving Medical Center 0 0 0 1 0 0 0 1
Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein 0 7 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 73
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_000335.5(SCN5A):c.3305C>A (p.Ser1102Tyr) rs7626962 0.02208
NM_000243.3(MEFV):c.2118G>A (p.Pro706=) rs2234939 0.00864
NM_000335.5(SCN5A):c.4215G>A (p.Gly1405=) rs41311123 0.00859
NM_000492.4(CFTR):c.4272C>T (p.Tyr1424=) rs1800135 0.00660
NM_000518.5(HBB):c.93-23T>C rs111851677 0.00593
NM_000243.3(MEFV):c.42G>A (p.Glu14=) rs113314808 0.00369
NM_001065.4(TNFRSF1A):c.1110C>T (p.Arg370=) rs201683984 0.00236
NM_000492.4(CFTR):c.2991G>C (p.Leu997Phe) rs1800111 0.00208
NM_000371.4(TTR):c.360C>T (p.Ser120=) rs150127220 0.00128
NM_004004.6(GJB2):c.478G>A (p.Gly160Ser) rs34988750 0.00107
NM_000371.4(TTR):c.417G>A (p.Thr139=) rs2276382 0.00104
NM_000492.4(CFTR):c.3897A>G (p.Thr1299=) rs1800131 0.00101
NM_000335.5(SCN5A):c.3266C>T (p.Pro1089Leu) rs1805125 0.00071
NM_001065.4(TNFRSF1A):c.789T>C (p.Thr263=) rs201290189 0.00069
NM_000243.3(MEFV):c.2149C>T (p.Arg717Cys) rs104895192 0.00066
NM_000492.4(CFTR):c.509G>A (p.Arg170His) rs1800079 0.00045
NM_001065.4(TNFRSF1A):c.645C>T (p.Pro215=) rs147075345 0.00020
NM_000435.3(NOTCH3):c.1690G>A (p.Ala564Thr) rs374767079 0.00013
NM_000335.5(SCN5A):c.5364C>T (p.Asp1788=) rs375752426 0.00011
NM_002016.2(FLG):c.4544C>A (p.Ser1515Ter) rs180768115 0.00006
NM_000435.3(NOTCH3):c.451C>G (p.Gln151Glu) rs371491165 0.00005
NM_001163435.3(TBCK):c.2060-2A>G rs62321379 0.00005
NM_000371.4(TTR):c.262A>T (p.Ile88Leu) rs121918085 0.00004
NM_000243.3(MEFV):c.1758T>C (p.Asn586=) rs202228332 0.00003
NM_000371.4(TTR):c.70-9T>C rs764059061 0.00003
NM_000243.3(MEFV):c.149C>T (p.Pro50Leu) rs144716190 0.00001
NM_000243.3(MEFV):c.540G>C (p.Pro180=) rs104895139 0.00001
NM_000435.3(NOTCH3):c.619C>T (p.Arg207Cys) rs775267348 0.00001
NM_000492.4(CFTR):c.1517T>C (p.Ile506Thr) rs397508224 0.00001
NM_000527.5(LDLR):c.1576C>T (p.Pro526Ser) rs730882106 0.00001
NM_000540.3(RYR1):c.983G>A (p.Arg328Gln) rs755875230 0.00001
NM_001253852.3(AP4B1):c.1216C>T (p.Arg406Ter) rs776976178 0.00001
NM_004525.3(LRP2):c.2639+1G>A rs746752313 0.00001
NM_014639.4(SKIC3):c.1499G>T (p.Gly500Val) rs138144509 0.00001
NM_000044.6(AR):c.2086G>A (p.Asp696Asn) rs1555995840
NM_000314.8(PTEN):c.71A>G (p.Asp24Gly) rs797044910
NM_000371.4(TTR):c.259G>C (p.Gly87Arg) rs11541799
NM_000371.4(TTR):c.272T>C (p.Val91Ala) rs121918084
NM_000371.4(TTR):c.325G>C (p.Glu109Gln) rs121918082
NM_000371.4(TTR):c.337-14_337-11del rs112263266
NM_000435.3(NOTCH3):c.120C>T (p.Ala40=) rs146904189
NM_000492.4(CFTR):c.1364C>T (p.Ala455Val) rs74551128
NM_000492.4(CFTR):c.3038C>T (p.Pro1013Leu) rs193922516
NM_000492.4(CFTR):c.473G>A (p.Ser158Asn) rs397508725
NM_000518.4(HBB):c.-92C>G rs397515291
NM_000518.5(HBB):c.380T>A (p.Val127Glu) rs33925391
NM_000518.5(HBB):c.4G>A (p.Val2Met) rs33958358
NM_000553.6(WRN):c.1165del (p.Arg389fs) rs878854131
NM_001032221.6(STXBP1):c.325+2_325+3del rs1554776853
NM_001065.4(TNFRSF1A):c.714G>A (p.Arg238=) rs200376188
NM_001144967.3(NEDD4L):c.2677G>A (p.Glu893Lys)
NM_001244008.2(KIF1A):c.173C>T (p.Ser58Leu) rs672601362
NM_001244008.2(KIF1A):c.604G>C (p.Ala202Pro) rs672601366
NM_001271.4(CHD2):c.2095C>T (p.Arg699Trp)
NM_001371928.1(AHDC1):c.2062C>T (p.Arg688Ter) rs1165205177
NM_001378452.1(ITPR1):c.7793T>C (p.Ile2598Thr) rs1553758021
NM_001429.4(EP300):c.4505C>T (p.Pro1502Leu) rs1555911573
NM_002834.5(PTPN11):c.417G>C (p.Glu139Asp) rs397507520
NM_003482.4(KMT2D):c.15143G>A (p.Arg5048His) rs886041404
NM_004975.4(KCNB1):c.629C>T (p.Thr210Met) rs1555889162
NM_005249.5(FOXG1):c.824G>C (p.Arg275Pro) rs1555321361
NM_006009.4(TUBA1A):c.1177C>T (p.His393Tyr) rs1555162288
NM_006087.4(TUBB4A):c.1172G>T (p.Arg391Leu) rs886041021
NM_007327.4(GRIN1):c.2381G>A (p.Arg794Gln) rs781053477
NM_013275.6(ANKRD11):c.2175_2178del (p.Asn725fs) rs886039734
NM_014639.4(SKIC3):c.2578-7_2578-3del rs746874042
NM_014927.5(CNKSR2):c.1282C>T (p.Arg428Ter) rs1064794022
NM_014946.4(SPAST):c.1496G>A (p.Arg499His) rs878854991
NM_015570.4(AUTS2):c.946C>T (p.Arg316Ter) rs1554480537
NM_020699.4(GATAD2B):c.1432C>T (p.Arg478Ter) rs761820222
NM_052867.4(NALCN):c.3542G>A (p.Arg1181Gln) rs786201003
NM_152564.5(VPS13B):c.5927del (p.Pro1976fs) rs755125969
NM_152564.5(VPS13B):c.901_904del (p.Thr301fs) rs759536357

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