ClinVar Miner

Variants from Lupski Lab, Baylor-Hopkins CMG,Baylor College of Medicine with conflicting interpretations

Location: United States — Primary collection method: research
Minimum review status of the submission from Lupski Lab, Baylor-Hopkins CMG,Baylor College of Medicine: Collection method of the submission from Lupski Lab, Baylor-Hopkins CMG,Baylor College 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 Variants with at least 2 submissions 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 kind of conflict
469 130 0 78 14 2 48 133

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
Lupski Lab, Baylor-Hopkins CMG,Baylor College of Medicine pathogenic likely pathogenic uncertain significance likely benign benign risk factor
pathogenic 0 22 12 2 2 0
likely pathogenic 59 0 20 7 10 1
uncertain significance 7 4 0 14 9 0
association 0 0 1 0 0 0

Submitter to submitter summary #

Total submitters: 59
Download table as spreadsheet
Submitter Variants with only 1 submission Variants with at least 2 submissions 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 kind of conflict
OMIM 0 92 0 48 0 1 8 56
GeneDx 0 35 0 17 7 0 12 36
Invitae 0 36 0 8 7 0 16 31
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics 0 9 0 6 7 0 9 22
Ambry Genetics 0 12 0 5 4 0 11 20
Illumina Clinical Services Laboratory,Illumina 0 5 0 2 8 1 6 17
Genetic Services Laboratory, University of Chicago 0 4 0 1 4 0 6 11
Laboratory for Molecular Medicine,Partners HealthCare Personalized Medicine 0 5 0 4 4 0 3 11
PreventionGenetics 0 0 0 0 6 0 2 8
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics 0 1 0 0 4 0 4 8
Integrated Genetics/Laboratory Corporation of America 0 3 0 3 2 0 1 6
Baylor Miraca Genetics Laboratories, 0 2 0 2 0 0 3 5
Athena Diagnostics Inc 0 2 0 1 4 0 0 5
Biesecker Lab/Human Development Section,National Institutes of Health 0 0 0 0 4 0 1 5
GeneReviews 0 11 0 4 0 0 0 4
Lupski Lab, Baylor-Hopkins CMG,Baylor College of Medicine 726 2 0 3 0 0 1 4
Counsyl 0 1 0 1 0 0 2 3
Fulgent Genetics 0 9 0 3 0 0 0 3
Developmental Genetics Unit,King Faisal Specialist Hospital & Research Centre 0 0 0 3 0 0 0 3
Institute of Human Genetics,Klinikum rechts der Isar 0 0 0 3 0 0 0 3
CeGaT Praxis fuer Humangenetik Tuebingen 0 3 0 0 0 0 3 3
Center for Human Genetics, Inc 0 3 0 2 0 0 0 2
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories 0 3 0 0 1 0 1 2
Genomic Research Center,Shahid Beheshti University of Medical Sciences 0 2 0 0 0 0 2 2
CSER_CC_NCGL; University of Washington Medical Center 0 3 0 0 0 0 2 2
Color 0 2 0 0 0 0 2 2
Human Genetics - Radboudumc,Radboudumc 0 0 0 1 0 0 1 2
CHEO Genetics Diagnostic Laboratory,Children's Hospital of Eastern Ontario 0 0 0 0 0 0 1 1
Division of Genomic Diagnostics,The Children's Hospital of Philadelphia 0 1 0 0 1 0 0 1
Mendelics 0 1 0 0 1 0 0 1
Mayo Clinic Genetic Testing Laboratories,Mayo Clinic 0 0 0 0 0 0 1 1
Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM) 0 0 0 1 0 0 0 1
Blueprint Genetics, 0 2 0 0 0 0 1 1
Wellcome Centre for Mitochondrial Research,Newcastle University 0 0 0 0 0 0 1 1
Institute of Human Genetics,Friedrich-Alexander-Universität Erlangen-Nürnberg 0 0 0 1 0 0 0 1
Agnes Ginges Centre for Molecular Cardiology,Centenary Institute 0 1 0 0 0 0 1 1
Stanford Center for Inherited Cardiovascular Disease,Stanford University 0 3 0 1 0 0 0 1
Division of Human Genetics,Children's Hospital of Philadelphia 0 0 0 1 0 0 0 1
Laboratory of Human Genetics,Universidade de São Paulo 0 0 0 0 1 0 0 1
HudsonAlpha Institute for Biotechnology 0 1 0 1 0 0 0 1
Knight Diagnostic Laboratories,Oregon Health and Sciences University 0 0 0 1 0 0 0 1
Laboratory of Genetics and Molecular Cardiology,University of São Paulo 0 2 0 0 0 0 1 1
Center of Genomic medicine, Geneva,University Hospital of Geneva 0 0 0 1 0 0 0 1
NeuroMeGen,Hospital Clinico Santiago de Compostela 0 0 0 1 0 0 0 1
Institute of Molecular Biology and Genetics,Federal Almazov North-West Medical Research Centre 0 0 0 1 0 0 0 1
Molecular Diagnostic Laboratory for Inherited Cardiovascular Disease,Montreal Heart Institute 0 2 0 0 0 0 1 1
Institute of Human Genetics, Univ. Regensburg,Univ. Regensburg 0 1 0 1 0 0 0 1
Database of Curated Mutations (DoCM) 0 0 0 0 0 0 1 1
NIHR Bioresource Rare Diseases,University of Cambridge 0 1 0 1 0 0 0 1
Undiagnosed Diseases Network,NIH 0 0 0 1 0 0 0 1
Demoulin lab,University of Louvain 0 1 0 1 0 0 0 1
Equipe Genetique des Anomalies du Developpement,Université de Bourgogne 0 1 0 0 1 0 0 1
SIB Swiss Institute of Bioinformatics 0 2 0 1 0 0 0 1
ClinGen Inherited Cardiomyopathy Variant Curation Expert Panel, 0 0 0 0 0 0 1 1
Wong Mito Lab, Molecular and Human Genetics,Baylor College of Medicine 0 1 0 1 0 0 0 1
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago 0 1 0 1 0 0 0 1
Diagnostic Laboratory, Department of Genetics,University Medical Center Groningen 0 2 0 0 1 0 0 1
Gharavi Laboratory,Columbia University 0 1 0 1 0 0 0 1
Biochemistry Laboratory of CDMU,Chengde Medical University 0 0 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 133
Download table as spreadsheet
HGVS dbSNP
NM_000153.3(GALC):c.1162-4delT rs11300320
NM_000170.2(GLDC):c.1940C>T (p.Pro647Leu) rs201135624
NM_000170.2(GLDC):c.2938A>G (p.Asn980Asp) rs772574530
NM_000216.3(ANOS1):c.2015A>G (p.His672Arg) rs199771303
NM_000218.2(KCNQ1):c.1189C>T (p.Arg397Trp) rs199472776
NM_000218.2(KCNQ1):c.724G>A (p.Asp242Asn) rs199472712
NM_000245.3(MET):c.2975C>T (p.Thr992Ile) rs56391007
NM_000257.3(MYH7):c.2389G>A (p.Ala797Thr) rs3218716
NM_000257.3(MYH7):c.728G>A (p.Arg243His) rs267606910
NM_000257.4(MYH7):c.4377G>T (p.Lys1459Asn) rs201307101
NM_000314.6(PTEN):c.464A>G (p.Tyr155Cys) rs1060500126
NM_000350.2(ABCA4):c.161G>A (p.Cys54Tyr) rs150774447
NM_000350.2(ABCA4):c.5882G>A rs1800553
NM_000350.2(ABCA4):c.6729+5_6729+19delGTTGGCCCTGGGGCA rs749526785
NM_000368.4(TSC1):c.2194C>T (p.His732Tyr) rs118203657
NM_000426.3(LAMA2):c.5530C>A (p.Arg1844Ser) rs56173620
NM_000441.1(SLC26A4):c.85G>C (p.Glu29Gln) rs111033205
NM_000503.5(EYA1):c.164C>T (p.Thr55Met) rs201434219
NM_000834.3(GRIN2B):c.2065G>A (p.Gly689Ser) rs869312868
NM_001009994.2(RIPPLY2):c.299delT (p.Leu100Argfs) rs864309489
NM_001012415.2(SOHLH1):c.27C>G (p.Tyr9Ter) rs864309646
NM_001012415.2(SOHLH1):c.705delT (p.Lys236Argfs) rs864309645
NM_001017995.2(SH3PXD2B):c.969delG (p.Arg324Glyfs) rs794728006
NM_001035.2(RYR2):c.8162T>C (p.Ile2721Thr) rs201500134
NM_001111125.2(IQSEC2):c.3364C>T (p.Arg1122Cys) rs782697291
NM_001127222.1(CACNA1A):c.5015G>C (p.Arg1672Pro) rs1057519429
NM_001130438.2(SPTAN1):c.1330G>A (p.Val444Ile) rs77358650
NM_001142279.2(RNASEH2B):c.356A>G (p.Asp119Gly) rs786205483
NM_001143905.2(C12orf65):c.248delT (p.Val83Glyfs) rs587776508
NM_001143996.1(OGDHL):c.2162C>T (p.Ser721Leu) rs773888308
NM_001160227.1(SPG11):c.5175delA (p.Ala1726Glnfs) rs1060499768
NM_001170535.2(ATAD3A):c.1582C>T (p.Arg528Trp) rs1057517686
NM_001170535.2(ATAD3A):c.158C>T (p.Thr53Ile) rs1057517687
NM_001190716.1(DNM2):c.1072G>A (p.Gly358Arg) rs267606772
NM_001199107.1(TBC1D24):c.328G>A (p.Gly110Ser) rs747821285
NM_001199107.1(TBC1D24):c.724C>T (p.Arg242Cys) rs398122965
NM_001201401.1(GALC):c.1918T>G (p.Trp640Gly) rs1060499761
NM_001267609.1(GPR161):c.56T>A (p.Leu19Gln) rs200635937
NM_001270399.1(TUBA1A):c.920C>T (p.Pro307Leu) rs1555162325
NM_001293212.1(TUBB):c.920C>T (p.Pro307Leu) rs1554202416
NM_001360.2(DHCR7):c.278C>T (p.Thr93Met) rs80338853
NM_001615.3(ACTG2):c.118C>T (p.Arg40Cys) rs587777385
NM_001615.3(ACTG2):c.119G>A (p.Arg40His) rs587777386
NM_001927.3(DES):c.638C>T (p.Ala213Val) rs41272699
NM_002108.3(HAL):c.1287+2T>C rs141634423
NM_002290.4(LAMA4):c.2377C>T (p.Arg793Cys) rs202184174
NM_002471.3(MYH6):c.3010G>T (p.Ala1004Ser) rs143978652
NM_002609.3(PDGFRB):c.1998C>A (p.Asn666Lys) rs864309711
NM_002677.5(PMP2):c.128T>A (p.Ile43Asn) rs879253869
NM_002677.5(PMP2):c.155T>C (p.Ile52Thr)
NM_002834.4(PTPN11):c.836A>G (p.Tyr279Cys) rs121918456
NM_002942.4(ROBO2):c.2431C>T (p.Arg811Trp) rs188582283
NM_002968.2(SALL1):c.469_477delAGCAGCAGC (p.Ser157_Ser159del) rs113614842
NM_003035.2(STIL):c.1455G>C (p.Leu485Phe) rs139912214
NM_003038.4(SLC1A4):c.1369C>T (p.Arg457Trp) rs761533681
NM_003172.3(SURF1):c.586C>T (p.Gln196Ter) rs147816470
NM_003384.2(VRK1):c.266G>A (p.Arg89Gln) rs773138218
NM_003384.2(VRK1):c.706G>A (p.Val236Met) rs771364038
NM_004463.2(FGD1):c.527dup (p.Leu177Thrfs) rs756586058
NM_004519.3(KCNQ3):c.688C>T (p.Arg230Cys) rs796052676
NM_004667.5(HERC2):c.12801T>A (p.Asp4267Glu) rs373175587
NM_005045.3(RELN):c.5156C>T (p.Ser1719Leu) rs115913736
NM_005045.3(RELN):c.5618C>T (p.Thr1873Ile) rs41275239
NM_005612.4(REST):c.1310T>A (p.Leu437Ter) rs1553904077
NM_005612.4(REST):c.2413delC (p.Leu805Phefs) rs1553904346
NM_005612.4(REST):c.2865_2866delAA (p.Asn958Serfs) rs1553904481
NM_005634.2(SOX3):c.157G>C (p.Val53Leu) rs200361128
NM_005641.3(TAF6):c.212T>C (p.Ile71Thr) rs374993554
NM_005654.5(NR2F1):c.335G>A (p.Arg112Lys) rs587777277
NM_005654.5(NR2F1):c.339C>A (p.Ser113Arg) rs587777275
NM_005654.5(NR2F1):c.344G>C (p.Arg115Pro) rs587777274
NM_005654.5(NR2F1):c.755T>C (p.Leu252Pro) rs587777276
NM_005781.4(TNK2):c.2630G>A (p.Arg877His) rs112384084
NM_005932.3(MIPEP):c.1745T>G (p.Leu582Arg) rs1057518739
NM_005932.3(MIPEP):c.212T>A (p.Leu71Gln) rs1057518740
NM_006295.2(VARS):c.2653C>T (p.Leu885Phe) rs1060499734
NM_006295.2(VARS):c.3173G>A (p.Arg1058Gln) rs769369302
NM_006439.4(MAB21L2):c.145G>A (p.Glu49Lys) rs587777513
NM_006439.4(MAB21L2):c.151C>T (p.Arg51Cys) rs587777512
NM_006439.4(MAB21L2):c.152G>A (p.Arg51His) rs587777511
NM_006439.4(MAB21L2):c.740G>A (p.Arg247Gln) rs587777514
NM_006567.4(FARS2):c.431A>G (p.Tyr144Cys) rs397514610
NM_006651.4(CPLX1):c.322G>T (p.Glu108Ter) rs1060499735
NM_006831.2(CLP1):c.419G>A (p.Arg140His) rs587777616
NM_007327.4(GRIN1):c.679G>C (p.Asp227His) rs869312865
NM_012102.3(RERE):c.4293C>A (p.His1431Gln) rs869312871
NM_012144.3(DNAI1):c.862C>T (p.Arg288Trp) rs202213517
NM_012160.4(FBXL4):c.419T>C (p.Val140Ala) rs1057519447
NM_014363.5(SACS):c.2182C>T (p.Arg728Ter) rs752059006
NM_014363.5(SACS):c.4466A>G (p.Asn1489Ser) rs147099630
NM_015047.2(EMC1):c.1411G>C (p.Gly471Arg) rs879253819
NM_015047.2(EMC1):c.245C>T (p.Thr82Met) rs869320625
NM_015047.2(EMC1):c.2602G>A (p.Gly868Arg) rs869320626
NM_015047.2(EMC1):c.2619_2622delTCCT (p.Pro874Argfs) rs869320624
NM_015114.2(ANKLE2):c.1717C>G (p.Leu573Val) rs863225465
NM_015271.4(TRIM2):c.2000A>C (p.Asp667Ala) rs879253863
NM_016188.5(ACTL6B):c.893G>A (p.Arg298Gln) rs1060499738
NM_016952.4(CDON):c.3395C>T (p.Pro1132Leu) rs754025360
NM_017721.4(CC2D1A):c.1739C>T (p.Thr580Ile) rs202057391
NM_017721.4(CC2D1A):c.2657G>A (p.Arg886His) rs201921029
NM_017882.2(CLN6):c.407G>A (p.Arg136His) rs769701646
NM_017890.4(VPS13B):c.1219C>T (p.Gln407Ter) rs386834070
NM_018055.4(NODAL):c.778G>A (p.Gly260Arg) rs121909283
NM_018136.4(ASPM):c.1729_1730delAG (p.Ser577Argfs) rs199422146
NM_020191.2(MRPS22):c.404G>A (p.Arg135Gln) rs774237195
NM_021222.1(PRUNE1):c.383G>A (p.Arg128Gln) rs767769359
NM_021222.2(PRUNE1):c.316G>A (p.Asp106Asn) rs773618224
NM_021222.2(PRUNE1):c.520G>T (p.Gly174Ter) rs200618384
NM_021222.2(PRUNE1):c.88G>A (p.Asp30Asn) rs1057521927
NM_021991.3(JUP):c.773A>G (p.Glu258Gly) rs794729052
NM_022835.2(PLEKHG2):c.1708G>A (p.Gly570Arg) rs370673772
NM_024596.4(MCPH1):c.427dupA (p.Thr143Asnfs) rs199422125
NM_032208.2(ANTXR1):c.1150G>A (p.Gly384Ser) rs869312897
NM_032208.2(ANTXR1):c.1221dupT (p.Ala408Cysfs) rs869312895
NM_032208.2(ANTXR1):c.411A>G (p.Gln137=) rs869312896
NM_032504.1(UNC80):c.2033delA (p.Asn678Thrfs) rs869025318
NM_032504.1(UNC80):c.5098C>T (p.Pro1700Ser) rs869025316
NM_032504.1(UNC80):c.7607G>C (p.Arg2536Thr) rs869025317
NM_032504.1(UNC80):c.7757T>A (p.Leu2586Ter) rs869025319
NM_033071.3(SYNE1):c.19479+3G>A rs150304757
NM_053067.2(UBQLN1):c.377delA (p.Asn126Metfs) rs1060499753
NM_139276.2(STAT3):c.1243G>A (p.Glu415Lys) rs193922717
NM_139276.2(STAT3):c.1261G>A (p.Gly421Arg) rs869312888
NM_139276.2(STAT3):c.2147C>T (p.Thr716Met) rs869312892
NM_144966.5(FREM1):c.1394G>C (p.Gly465Ala) rs41298151
NM_145812.2(AIFM1):c.1376G>T (p.Arg459Ile) rs202219398
NM_176787.4(PIGN):c.996T>G (p.Ile332Met) rs1060499763
NM_177438.2(DICER1):c.4050+1G>A rs875989783
NM_177550.4(SLC13A5):c.655G>A (p.Gly219Arg) rs144332569
NM_177550.4(SLC13A5):c.680C>T (p.Thr227Met) rs587777577
NM_181457.3(PAX3):c.944C>A (p.Thr315Lys) rs2234675
NM_198056.2(SCN5A):c.1567C>T (p.Arg523Cys) rs199473119
NM_198056.2(SCN5A):c.1705C>G (p.Arg569Gly) rs199473576

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