ClinVar Miner

Variants from Division of Human Genetics, Children's Hospital of Philadelphia with conflicting interpretations

Location: United States  Primary collection method: research
Minimum review status of the submission from Division of Human Genetics, Children's Hospital of Philadelphia: Collection method of the submission from Division of Human Genetics, Children's Hospital of Philadelphia:
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
123 75 0 78 17 4 30 112

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
Division of Human Genetics, Children's Hospital of Philadelphia pathogenic likely pathogenic uncertain significance likely benign benign pathogenic, low penetrance other
pathogenic 0 39 8 3 2 1 3
likely pathogenic 39 0 11 1 1 0 0
uncertain significance 5 5 0 15 4 0 0

Submitter to submitter summary #

Total submitters: 84
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 48 0 21 9 1 10 41
Fulgent Genetics, Fulgent Genetics 0 47 0 14 1 0 2 17
Baylor Genetics 0 42 0 13 0 0 1 14
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 0 30 0 10 1 0 3 14
Natera, Inc. 0 29 0 9 2 0 2 13
OMIM 0 32 0 6 0 3 2 11
Revvity Omics, Revvity 0 27 0 8 0 0 3 11
Illumina Laboratory Services, Illumina 0 43 0 7 1 0 3 11
Counsyl 0 9 0 7 0 0 3 10
Mendelics 0 15 0 4 0 0 3 7
Genome-Nilou Lab 0 18 0 5 0 0 2 7
Institute of Human Genetics, University of Leipzig Medical Center 0 14 0 4 0 0 2 6
Myriad Genetics, Inc. 0 22 0 5 0 0 1 6
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine 0 18 0 5 0 0 0 5
MGZ Medical Genetics Center 0 7 0 5 0 0 0 5
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute 0 18 0 5 0 0 0 5
Genetic Services Laboratory, University of Chicago 0 7 0 2 1 0 1 4
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories 0 6 0 1 1 0 2 4
Genomic Research Center, Shahid Beheshti University of Medical Sciences 0 4 0 3 0 0 1 4
Knight Diagnostic Laboratories, Oregon Health and Sciences University 0 13 0 4 0 0 0 4
PreventionGenetics, part of Exact Sciences 0 3 0 0 2 0 1 3
NIHR Bioresource Rare Diseases, University of Cambridge 0 1 0 1 0 0 2 3
Genetics and Molecular Pathology, SA Pathology 0 8 0 3 0 0 0 3
Wong Mito Lab, Molecular and Human Genetics, Baylor College of Medicine 0 1 0 2 0 0 1 3
Reproductive Health Research and Development, BGI Genomics 0 3 0 3 0 0 0 3
Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center 0 4 0 3 0 0 0 3
Genomics England Pilot Project, Genomics England 0 4 0 3 0 0 0 3
GeneDx 0 5 0 0 1 0 1 2
Ambry Genetics 0 6 0 1 1 0 0 2
Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia 0 2 0 0 0 0 2 2
Genome Diagnostics Laboratory, University Medical Center Utrecht 0 8 0 2 0 0 0 2
HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology 0 4 0 2 0 0 0 2
Center of Genomic medicine, Geneva, University Hospital of Geneva 0 2 0 1 0 0 1 2
Undiagnosed Diseases Network, NIH 0 3 0 2 0 0 0 2
Seattle Children's Hospital Molecular Genetics Laboratory, Seattle Children's Hospital 0 0 0 2 0 0 0 2
Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard 0 4 0 0 0 0 2 2
Lifecell International Pvt. Ltd 0 4 0 1 0 0 1 2
ISTH-SSC Genomics in Thrombosis and Hemostasis, KU Leuven, Center for Molecular and Vascular Biology 0 0 0 2 0 0 0 2
All of Us Research Program, National Institutes of Health 0 2 0 1 1 0 0 2
Athena Diagnostics Inc 0 1 0 0 0 0 1 1
Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center 0 12 0 1 0 0 0 1
King Laboratory, University of Washington 0 0 0 0 0 0 1 1
Elsea Laboratory, Baylor College of Medicine 0 0 0 0 0 0 1 1
Centogene AG - the Rare Disease Company 0 12 0 1 0 0 0 1
ClinVar Staff, National Center for Biotechnology Information (NCBI) 0 0 0 0 0 0 1 1
Blueprint Genetics 0 0 0 0 0 0 1 1
Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München 0 5 0 1 0 0 0 1
Clinical Genomics Laboratory, Washington University in St. Louis 0 2 0 1 0 0 0 1
UCLA Clinical Genomics Center, UCLA 0 0 0 1 0 0 0 1
Hadassah Hebrew University Medical Center 0 2 0 1 0 0 0 1
CeGaT Center for Human Genetics Tuebingen 0 3 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
Centre for Mendelian Genomics, University Medical Centre Ljubljana 0 5 0 0 0 0 1 1
Centre de Génétique Moléculaire et Chromosomique, Unité de génétique de l'Obésité et des Dyslipidémies, APHP, GH Hôpitaux Universitaires Pitié-Salpêtrière / Charles-Foix 0 0 0 0 0 0 1 1
Equipe Genetique des Anomalies du Developpement, Université de Bourgogne 0 4 0 1 0 0 0 1
Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego 0 8 0 1 0 0 0 1
SIB Swiss Institute of Bioinformatics 0 1 0 1 0 0 0 1
Department of Pathology and Laboratory Medicine, Sinai Health System 0 1 0 0 0 0 1 1
Leiden Open Variation Database 0 0 0 1 0 0 0 1
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago 0 5 0 1 0 0 0 1
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen 0 8 0 0 1 0 0 1
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center 0 6 0 1 0 0 0 1
SingHealth Duke-NUS Institute of Precision Medicine 0 0 0 0 0 0 1 1
ClinGen PAH Variant Curation Expert Panel 0 3 0 1 0 0 0 1
Ocular Genomics Institute, Massachusetts Eye and Ear 0 0 0 1 0 0 0 1
UNC Molecular Genetics Laboratory, University of North Carolina at Chapel Hill 0 7 0 1 0 0 0 1
Johns Hopkins Genomics, Johns Hopkins University 0 10 0 1 0 0 0 1
Genetic Testing Center for Deafness, Department of Otolaryngology Head & Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital 0 1 0 1 0 0 0 1
ClinGen Myeloid Malignancy Variant Curation Expert Panel 0 0 0 1 0 0 0 1
Al Jalila Children's Genomics Center, Al Jalila Childrens Speciality Hospital 0 2 0 1 0 0 0 1
Zotz-Klimas Genetics Lab, MVZ Zotz Klimas 0 4 0 1 0 0 0 1
Genomics Facility, Ludwig-Maximilians-Universität München 0 0 0 1 0 0 0 1
Clinical Genomics Program, Stanford Medicine 0 2 0 1 0 0 0 1
Institute of Human Genetics, University Hospital Muenster 0 3 0 1 0 0 0 1
AiLife Diagnostics, AiLife Diagnostics 0 1 0 0 0 0 1 1
GenomeConnect - Simons Searchlight 0 0 0 1 0 0 0 1
3billion 0 9 0 1 0 0 0 1
Suma Genomics 0 4 0 0 0 0 1 1
DASA 0 8 0 1 0 0 0 1
Neuberg Centre For Genomic Medicine, NCGM 0 5 0 1 0 0 0 1
H3Africa Consortium 0 0 0 0 0 0 1 1
European Hospital Georges Pompidou Genetics Department, Assistance Publique - Hôpitaux de Paris AP-HP 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
Dunham Lab, University of Washington 0 1 0 0 0 0 1 1

All variants with conflicting interpretations #

Total variants: 112
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_000402.4(G6PD):c.466A>G (p.Asn156Asp) rs1050829 0.08672
NM_000155.4(GALT):c.940A>G (p.Asn314Asp) rs2070074 0.07150
NM_000402.4(G6PD):c.292G>A (p.Val98Met) rs1050828 0.03616
NM_001370658.1(BTD):c.1270G>C (p.Asp424His) rs13078881 0.03225
NM_001127701.1(SERPINA1):c.863A>T (p.Glu288Val) rs17580 0.02950
NM_000518.5(HBB):c.20A>T (p.Glu7Val) rs334 0.01298
NM_004004.6(GJB2):c.101T>C (p.Met34Thr) rs35887622 0.00966
NM_004004.6(GJB2):c.109G>A (p.Val37Ile) rs72474224 0.00354
NM_000275.3(OCA2):c.1327G>A (p.Val443Ile) rs121918166 0.00350
NM_001384474.1(LOXHD1):c.5802C>A (p.Asn1934Lys) rs61733519 0.00316
NM_001089.3(ABCA3):c.875A>T (p.Glu292Val) rs149989682 0.00304
NM_001384474.1(LOXHD1):c.1570C>T (p.Arg524Cys) rs192376005 0.00295
NM_001001548.3(CD36):c.429+2T>C rs3211893 0.00220
NM_000478.6(ALPL):c.571G>A (p.Glu191Lys) rs121918007 0.00200
NM_000157.4(GBA1):c.1226A>G (p.Asn409Ser) rs76763715 0.00191
NM_007254.4(PNKP):c.416G>A (p.Arg139His) rs34472250 0.00185
NM_153700.2(STRC):c.4918C>T (p.Leu1640Phe) rs2920791 0.00174
NM_002693.3(POLG):c.1760C>T (p.Pro587Leu) rs113994096 0.00160
NM_002693.3(POLG):c.752C>T (p.Thr251Ile) rs113994094 0.00159
NM_001041.4(SI):c.3218G>A (p.Gly1073Asp) rs121912616 0.00150
NM_001041.4(SI):c.1730T>G (p.Val577Gly) rs121912615 0.00131
NM_032578.4(MYPN):c.59A>G (p.Tyr20Cys) rs140148105 0.00130
NM_001134363.3(RBM20):c.1286T>C (p.Leu429Pro) rs61735272 0.00126
NM_000552.5(VWF):c.1922C>T (p.Ala641Val) rs61754019 0.00098
NM_002693.3(POLG):c.2209G>C (p.Gly737Arg) rs121918054 0.00096
NM_000782.5(CYP24A1):c.1186C>T (p.Arg396Trp) rs114368325 0.00079
NM_000174.5(GP9):c.182A>G (p.Asn61Ser) rs5030764 0.00076
NM_000235.4(LIPA):c.894G>A (p.Gln298=) rs116928232 0.00075
NM_005609.4(PYGM):c.1094C>T (p.Ala365Val) rs116135678 0.00074
NM_001360.3(DHCR7):c.452G>A (p.Trp151Ter) rs11555217 0.00072
NM_001384474.1(LOXHD1):c.4480C>T (p.Arg1494Ter) rs201587138 0.00069
NM_006267.5(RANBP2):c.3226T>G (p.Leu1076Val) rs142768885 0.00068
NM_153676.4(USH1C):c.2167C>T (p.Gln723Ter) rs146451547 0.00068
NM_206933.4(USH2A):c.10073G>A (p.Cys3358Tyr) rs148660051 0.00056
NM_000277.3(PAH):c.734T>C (p.Val245Ala) rs76212747 0.00049
NM_017636.4(TRPM4):c.2674C>T (p.Arg892Cys) rs147854826 0.00047
NM_001035.3(RYR2):c.1822C>T (p.His608Tyr) rs727504718 0.00046
NM_001370658.1(BTD):c.1308A>C (p.Gln436His) rs80338685 0.00046
NM_006949.4(STXBP2):c.568C>T (p.Arg190Cys) rs370053399 0.00041
NM_001292063.2(OTOG):c.2464C>T (p.Gln822Ter) rs554847663 0.00040
NM_025137.4(SPG11):c.1270C>A (p.Pro424Thr) rs141596008 0.00040
NM_014249.4(NR2E3):c.119-2A>C rs2723341 0.00038
NM_001609.4(ACADSB):c.303+1G>A rs147936696 0.00037
NM_000277.3(PAH):c.1139C>T (p.Thr380Met) rs62642937 0.00036
NM_000277.3(PAH):c.194T>C (p.Ile65Thr) rs75193786 0.00032
NM_020451.3(SELENON):c.943G>A (p.Gly315Ser) rs121908188 0.00030
NM_000744.7(CHRNA4):c.274G>C (p.Glu92Gln) rs146651027 0.00029
NM_000402.4(G6PD):c.653C>T (p.Ser218Phe) rs5030868 0.00028
NM_000466.3(PEX1):c.2528G>A (p.Gly843Asp) rs61750420 0.00025
NM_024422.6(DSC2):c.2587G>A (p.Gly863Arg) rs147109895 0.00023
NM_031889.3(ENAM):c.1259_1260insAG (p.Pro422fs) rs587776588 0.00018
NM_172250.3(MMAA):c.433C>T (p.Arg145Ter) rs104893851 0.00017
NM_001134363.3(RBM20):c.2014G>A (p.Gly672Ser) rs730880182 0.00016
NM_000112.4(SLC26A2):c.1957T>A (p.Cys653Ser) rs104893924 0.00014
NM_001126108.2(SLC12A3):c.1928C>T (p.Pro643Leu) rs140012781 0.00014
NM_000035.4(ALDOB):c.911G>A (p.Arg304Gln) rs145078268 0.00013
NM_001369.3(DNAH5):c.4361G>A (p.Arg1454Gln) rs542708170 0.00013
NM_000170.3(GLDC):c.499G>T (p.Glu167Ter) rs191905539 0.00012
NM_000337.6(SGCD):c.451T>G (p.Ser151Ala) rs121909298 0.00012
NM_005751.5(AKAP9):c.610G>A (p.Asp204Asn) rs148920964 0.00011
NM_000090.4(COL3A1):c.2242G>A (p.Gly748Ser) rs771585795 0.00008
NM_001126108.2(SLC12A3):c.2864G>A (p.Arg955Gln) rs202114767 0.00008
NM_000173.7(GP1BA):c.256C>T (p.Leu86Phe) rs13306411 0.00007
NM_000642.3(AGL):c.3980G>A (p.Trp1327Ter) rs267606640 0.00006
NM_012452.3(TNFRSF13B):c.492C>G (p.Tyr164Ter) rs72553882 0.00006
NM_000219.6(KCNE1):c.226G>A (p.Asp76Asn) rs74315445 0.00005
NM_016239.4(MYO15A):c.5925G>A (p.Trp1975Ter) rs375290498 0.00005
NM_000083.3(CLCN1):c.920T>C (p.Phe307Ser) rs80356701 0.00004
NM_000527.5(LDLR):c.1003G>A (p.Gly335Ser) rs544453230 0.00004
NM_001360.3(DHCR7):c.461C>G (p.Thr154Arg) rs143312232 0.00003
NM_002471.4(MYH6):c.3508G>A (p.Glu1170Lys) rs727503236 0.00003
NM_015506.3(MMACHC):c.566G>A (p.Arg189His) rs761221416 0.00003
NM_000303.3(PMM2):c.255+1G>A rs1060499598 0.00002
NM_000540.3(RYR1):c.6838G>A (p.Val2280Ile) rs193922797 0.00002
NM_030777.4(SLC2A10):c.692G>A (p.Arg231Gln) rs771028960 0.00002
NM_138694.4(PKHD1):c.2854G>A (p.Gly952Arg) rs773136605 0.00002
NM_000277.3(PAH):c.1184C>G (p.Ala395Gly) rs62508736 0.00001
NM_000335.5(SCN5A):c.5347G>A (p.Glu1783Lys) rs137854601 0.00001
NM_000363.5(TNNI3):c.485G>A (p.Arg162Gln) rs397516354 0.00001
NM_000404.4(GLB1):c.245+1G>A rs778423653 0.00001
NM_000642.3(AGL):c.664+3A>G rs370792293 0.00001
NM_005609.4(PYGM):c.1726C>T (p.Arg576Ter) rs119103255 0.00001
NM_007294.4(BRCA1):c.5503C>T (p.Arg1835Ter) rs41293465 0.00001
NM_000018.4(ACADVL):c.1593dup (p.Ser532fs) rs1060499596
NM_000038.6(APC):c.904C>T (p.Arg302Ter) rs137854568
NM_000053.4(ATP7B):c.1374_1377del (p.Val459fs) rs1060499593
NM_000136.3(FANCC):c.356_360del (p.Ser119fs) rs1060499606
NM_000218.3(KCNQ1):c.513C>A (p.Tyr171Ter) rs139042529
NM_000249.4(MLH1):c.1943C>T (p.Pro648Leu) rs63750610
NM_000271.5(NPC1):c.3175C>T (p.Arg1059Ter) rs786204455
NM_000414.4(HSD17B4):c.1369A>T (p.Asn457Tyr) rs137853097
NM_000642.3(AGL):c.118C>T (p.Gln40Ter) rs771961377
NM_000720.4(CACNA1D):c.1208G>A (p.Gly403Asp) rs386834264
NM_001029896.2(WDR45):c.397C>T (p.Arg133Ter) rs797046101
NM_001035.3(RYR2):c.239A>G (p.Glu80Gly) rs794728706
NM_001098671.2(RASGRP2):c.542T>C (p.Phe181Ser) rs1060499609
NM_001099274.3(TINF2):c.81C>A (p.Cys27Ter) rs1060499576
NM_001127644.2(GABRA1):c.799C>A (p.Leu267Ile) rs796052492
NM_001360.3(DHCR7):c.964-1G>C rs138659167
NM_001754.5(RUNX1):c.497G>A (p.Arg166Gln) rs1060499616
NM_002016.2(FLG):c.1501C>T (p.Arg501Ter) rs61816761
NM_003764.4(STX11):c.391C>T (p.Gln131Ter) rs794729649
NM_004086.3(COCH):c.1625G>T (p.Cys542Phe) rs121908932
NM_004415.4(DSP):c.928dup (p.Glu310fs) rs794728137
NM_005476.7(GNE):c.2086G>A (p.Val696Met) rs121908627
NM_012434.5(SLC17A5):c.409del (p.Met137fs) rs794729653
NM_024685.4(BBS10):c.1677C>A (p.Tyr559Ter) rs375413604
NM_030632.3(ASXL3):c.1471C>T (p.Gln491Ter) rs1060499602
NM_032193.4(RNASEH2C):c.178dup (p.Glu60fs) rs772940104
NM_152443.3(RDH12):c.63_66del (p.Ile22fs) rs794729650
NM_153700.2(STRC):c.4917_4918delinsCT (p.Leu1640Phe) rs727503441
NM_183235.3(RAB27A):c.514_518del (p.Gln172fs) rs767481076

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