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 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
672 146 0 49 9 1 33 87

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 drug response protective other
pathogenic 0 15 6 3 3 1 1 1
likely pathogenic 37 0 11 7 7 0 0 0
uncertain significance 5 5 0 5 6 1 1 1

Submitter to submitter summary #

Total submitters: 78
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 84 0 26 0 0 5 31
Invitae 0 26 0 4 4 0 10 17
Baylor Genetics 0 9 0 6 0 0 3 8
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics 0 1 0 2 1 1 7 8
Illumina Clinical Services Laboratory,Illumina 0 6 0 0 6 0 3 8
CeGaT Praxis fuer Humangenetik Tuebingen 0 1 0 1 1 0 7 8
Genetic Services Laboratory, University of Chicago 0 3 0 1 0 0 6 7
GeneDx 0 5 0 3 1 0 5 7
Athena Diagnostics Inc 0 0 0 0 1 0 5 5
Ambry Genetics 0 0 0 0 0 0 4 4
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics 0 0 0 0 0 0 4 4
Biochemical Molecular Genetic Laboratory,King Abdulaziz Medical City 0 1 0 4 0 0 0 4
University of Washington Center for Mendelian Genomics, University of Washington 0 14 0 1 0 0 3 3
Lupski Lab, Baylor-Hopkins CMG, Baylor College of Medicine 900 2 0 3 0 0 1 3
Department of Pathology and Laboratory Medicine,Sinai Health System 0 0 0 0 0 0 3 3
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories 0 1 0 0 0 0 2 2
Mayo Clinic Laboratories, Mayo Clinic 0 0 0 1 0 0 2 2
Fulgent Genetics,Fulgent Genetics 0 6 0 2 0 0 0 2
HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology 0 1 0 1 0 0 1 2
Equipe Genetique des Anomalies du Developpement, Université de Bourgogne 0 2 0 2 0 0 1 2
SIB Swiss Institute of Bioinformatics 0 1 0 1 0 0 1 2
New York Genome Center 0 0 0 0 0 0 2 2
Center for Human Genetics, Inc,Center for Human Genetics, Inc 0 2 0 1 0 0 0 1
Medical Genetics Laboratory, Kennedy Center,Juliane Marie Center, Rigshospitalet 0 0 0 1 0 0 0 1
Laboratory for Molecular Medicine,Partners HealthCare Personalized Medicine 0 1 0 1 0 0 0 1
Elsea Laboratory,Baylor College of Medicine 0 0 0 0 0 0 1 1
Institute of Human Genetics,Cologne University 0 0 0 0 0 0 1 1
Counsyl 0 0 0 0 0 0 1 1
Integrated Genetics/Laboratory Corporation of America 0 2 0 0 0 0 1 1
Mendelics 0 5 0 1 0 0 0 1
Developmental Genetics Unit,King Faisal Specialist Hospital & Research Centre 0 0 0 1 0 0 1 1
Institute of Human Genetics, Klinikum rechts der Isar 0 3 0 1 0 0 0 1
Department of Psychiatry,Nagoya University 0 0 0 1 0 0 1 1
Center for Medical Genetics Ghent,University of Ghent 0 0 0 1 0 0 1 1
Vavilov Institute of General Genetics RAS, Laboratory of Evolutional Genomics 0 0 0 0 0 1 0 1
Lyon Laboratory, Cold Spring Harbor Laboratory 0 0 0 0 0 0 1 1
Knight Diagnostic Laboratories, Oregon Health and Sciences University 0 0 0 1 0 0 0 1
Genome Sciences Centre,British Columbia Cancer Agency 0 0 0 1 0 0 1 1
Oxford Medical Genetics Laboratories,Oxford University Hospitals NHS Foundation Trust 0 0 0 0 0 0 1 1
Centre de Biologie Pathologie Génétique, Centre Hospitalier Universitaire de Lille 0 0 0 1 0 0 0 1
Institute of Human Genetics, Univ. Regensburg,Univ. Regensburg 0 1 0 1 0 0 0 1
Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences 0 1 0 1 0 0 0 1
Centre for Mendelian Genomics,University Medical Centre Ljubljana 0 4 0 0 0 0 1 1
Pediatric Highly Intensive Care Unit,Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico 0 0 0 0 0 0 1 1
Daryl Scott Lab,Baylor College of Medicine 0 0 0 0 0 0 1 1
Neurogenetics Laboratory - MEYER,AOU Meyer 0 0 0 0 0 0 1 1
NIHR Bioresource Rare Diseases, University of Cambridge 0 1 0 1 0 0 1 1
Undiagnosed Diseases Network,NIH 0 0 0 1 0 0 1 1
Demoulin lab,University of Louvain 0 1 0 1 0 0 0 1
The Genetics Institute,Rambam Health Care Campus 0 0 0 0 0 0 1 1
Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego 0 3 0 0 0 0 1 1
Institute of Human Genetics, University of Leipzig Medical Center 0 1 0 1 0 0 0 1
Laboratoires de Diagnostic Génétique, Hôpitaux Universitaires de Strasbourg 0 0 0 1 0 0 0 1
Geisinger Autism and Developmental Medicine Institute,Geisinger Health System 0 0 0 1 1 0 1 1
Rare Disease Group, Clinical Genetics,Karolinska Institutet 0 0 0 1 1 0 1 1
Institute of Cellular and Molecular Medicine,Copenhagen University 0 0 0 1 0 0 1 1
Flegel Lab,National Institutes of Health 0 0 0 0 0 0 1 1
Sharon lab,Hadassah-Hebrew University Medical Center 0 0 0 1 0 0 0 1
Wong Mito Lab, Molecular and Human Genetics, Baylor College of Medicine 0 1 0 1 0 0 0 1
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen 0 0 0 0 1 0 0 1
Laboratoire de Genetique Moleculaire,Centre Hospitalier Universitaire de Bordeaux 0 0 0 0 0 0 1 1
Medical Genetics Lab,Policlinico S. Orsola.Malpighi 0 0 0 1 0 0 1 1
Medical Cytogenetics and Molecular Genetics Laboratory,IRCCS Istituto Auxologico Italiano 0 0 0 0 1 0 1 1
Broad Institute Rare Disease Group, Broad Institute 0 1 0 1 0 0 0 1
UNC Molecular Genetics Laboratory,University of North Carolina at Chapel Hill 0 0 0 1 0 0 0 1
Michaelson Lab,University of Iowa 0 0 0 0 0 0 1 1
Pathology and Clinical Laboratory Medicine,King Fahad Medical City 0 0 0 1 0 0 0 1
Molecular Pathology Diagnostics Labratory,University of Iowa Hospitals & Clinics 0 0 0 1 0 0 1 1
Coyote Medical Laboratory (Beijing),Coyote 0 0 0 1 0 0 0 1
Biochemistry Laboratory of CDMU,Chengde Medical University 0 0 0 1 0 0 1 1
Reproductive Health Research and Development,BGI Genomics 0 0 0 0 0 0 1 1
UT Southwestern Medical Center, UT Southwestern Medical Center 0 0 0 0 0 1 0 1
Autoinflammatory diseases unit,CHU de Montpellier 0 0 0 1 0 0 0 1
Central Laboratory,The First Hospital of Lanzhou University 0 0 0 0 0 0 1 1
Suna and Inan Kirac Foundation Neurodegeneration Research Laboratory, Koc University 0 0 0 0 0 0 1 1
Genetics and Prenatal Diagnosis Center,The First Affiliated Hospital of Zhengzhou University 0 0 0 1 0 0 1 1
Dept. Genetics and Cancer, Menzies Institute for Medical Research,University of Tasmania 0 0 0 0 1 0 1 1
Wilkie Group, Clinical Genetics Lab, WIMM,University of Oxford 0 0 0 0 0 0 1 1

All variants with conflicting interpretations #

Total variants: 87
Download table as spreadsheet
HGVS dbSNP
NM_000153.4(GALC):c.1162-4del rs11300320
NM_000216.4(ANOS1):c.2015A>G (p.His672Arg) rs199771303
NM_000350.2(ABCA4):c.5882G>A rs1800553
NM_000368.5(TSC1):c.2194C>T (p.His732Tyr) rs118203657
NM_000941.3(POR):c.859G>C (p.Ala287Pro) rs121912974
NM_001017995.3(SH3PXD2B):c.969del (p.Arg324fs) rs794728006
NM_001031710.3(KLHL7):c.1258C>T (p.Arg420Cys) rs780705654
NM_001039803.2(CDK20):c.610T>C (p.Phe204Leu) rs745561217
NM_001048166.1(STIL):c.1455G>C (p.Leu485Phe) rs139912214
NM_001106.4(ACVR2B):c.1147C>T (p.Arg383Cys) rs1559655653
NM_001111125.3(IQSEC2):c.3364C>T (p.Arg1122Cys) rs782697291
NM_001128929.3(ROBO2):c.2479C>T (p.Arg827Trp) rs188582283
NM_001130438.3(SPTAN1):c.1330G>A (p.Val444Ile) rs77358650
NM_001142279.2(RNASEH2B):c.356A>G (p.Asp119Gly) rs786205483
NM_001163817.2(DHCR7):c.278C>T (p.Thr93Met) rs80338853
NM_001170535.3(ATAD3A):c.158C>T (p.Thr53Ile) rs1057517687
NM_001243996.3(RYR3):c.2486G>A (p.Arg829His) rs199500216
NM_001271208.2(NEB):c.19101+5G>A rs374929094
NM_001271208.2(NEB):c.25093C>T (p.Arg8365Ter) rs767709270
NM_001278716.2(FBXL4):c.419T>C (p.Val140Ala) rs1057519447
NM_001330311.2(DVL1):c.1687_1691dup (p.Ser564fs) rs1553173372
NM_001366722.1(GRIP1):c.160G>A (p.Val54Ile) rs199768740
NM_002470.4(MYH3):c.2015G>A (p.Arg672His) rs121913617
NM_002609.4(PDGFRB):c.1998C>A (p.Asn666Lys) rs864309711
NM_002677.5(PMP2):c.155T>C (p.Ile52Thr) rs1563518388
NM_002709.3(PPP1CB):c.146C>G (p.Pro49Arg) rs886037952
NM_002834.5(PTPN11):c.836A>G (p.Tyr279Cys) rs121918456
NM_003384.3(VRK1):c.266G>A (p.Arg89Gln) rs773138218
NM_003392.7(WNT5A):c.461G>T (p.Cys154Phe)
NM_003491.4(NAA10):c.215T>C (p.Ile72Thr) rs1057519448
NM_003680.3(YARS1):c.586G>C (p.Glu196Gln) rs121908834
NM_004321.7(KIF1A):c.304G>A (p.Gly102Ser) rs1064795534
NM_004463.3(FGD1):c.527dup (p.Leu177fs) rs756586058
NM_004519.4(KCNQ3):c.688C>T (p.Arg230Cys) rs796052676
NM_004826.4(ECEL1):c.1210C>T (p.Arg404Cys) rs532757890
NM_004826.4(ECEL1):c.2023G>A (p.Ala675Thr) rs606231471
NM_005045.4(RELN):c.5156C>T (p.Ser1719Leu) rs115913736
NM_005045.4(RELN):c.5618C>T (p.Thr1873Ile) rs41275239
NM_005199.5(CHRNG):c.715C>T (p.Arg239Cys) rs121912670
NM_005634.2(SOX3):c.157G>C (p.Val53Leu) rs200361128
NM_005654.6(NR2F1):c.335G>A (p.Arg112Lys) rs587777277
NM_005654.6(NR2F1):c.339C>A (p.Ser113Arg) rs587777275
NM_005654.6(NR2F1):c.344G>C (p.Arg115Pro) rs587777274
NM_005654.6(NR2F1):c.755T>C (p.Leu252Pro) rs587777276
NM_006439.5(MAB21L2):c.145G>A (p.Glu49Lys) rs587777513
NM_006439.5(MAB21L2):c.151C>T (p.Arg51Cys) rs587777512
NM_006439.5(MAB21L2):c.152G>A (p.Arg51His) rs587777511
NM_006439.5(MAB21L2):c.740G>A (p.Arg247Gln) rs587777514
NM_006567.5(FARS2):c.431A>G (p.Tyr144Cys) rs397514610
NM_006757.4(TNNT3):c.187C>T (p.Arg63Cys) rs199474721
NM_006831.3(CLP1):c.419G>A (p.Arg140His) rs587777616
NM_012090.5(MACF1):c.16131T>G (p.Phe5377Leu) rs138819868
NM_012144.4(DNAI1):c.862C>T (p.Arg288Trp) rs202213517
NM_013438.5(UBQLN1):c.377del (p.Asn126fs) rs1060499753
NM_014362.4(HIBCH):c.410C>T (p.Ala137Val) rs1114167288
NM_014363.6(SACS):c.2182C>T (p.Arg728Ter) rs752059006
NM_014363.6(SACS):c.4466A>G (p.Asn1489Ser) rs147099630
NM_015271.5(TRIM2):c.2000A>C (p.Asp667Ala) rs879253863
NM_016952.4(CDON):c.3395C>T (p.Pro1132Leu) rs754025360
NM_017721.5(CC2D1A):c.1739C>T (p.Thr580Ile) rs202057391
NM_017721.5(CC2D1A):c.2657G>A (p.Arg886His) rs201921029
NM_017882.3(CLN6):c.407G>A (p.Arg136His) rs769701646
NM_018076.5(ODAD2):c.2219G>A (p.Trp740Ter) rs201213030
NM_018076.5(ODAD2):c.2780T>G (p.Leu927Trp) rs587777047
NM_018245.3(OGDHL):c.2333C>T (p.Ser778Leu) rs773888308
NM_018486.3(HDAC8):c.356C>T (p.Thr119Met) rs587779380
NM_021222.3(PRUNE1):c.316G>A (p.Asp106Asn) rs773618224
NM_021625.4(TRPV4):c.806G>A (p.Arg269His) rs267607144
NM_022835.3(PLEKHG2):c.1708G>A (p.Gly570Arg) rs370673772
NM_024072.4(DDX54):c.892C>T (p.Leu298Phe) rs1593005589
NM_032208.2(ANTXR1):c.1150G>A (p.Gly384Ser) rs869312897
NM_032208.2(ANTXR1):c.1221dup (p.Ala408fs) rs869312895
NM_032208.2(ANTXR1):c.411A>G (p.Gln137=) rs869312896
NM_032504.1(UNC80):c.2033del (p.Asn678fs) 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_032590.5(KDM2B):c.3050G>A (p.Arg1017His) rs782304760
NM_032656.4(DHX37):c.1399C>G (p.Leu467Val) rs149331610
NM_177550.4(SLC13A5):c.1475T>C (p.Leu492Pro) rs1057519449
NM_177550.4(SLC13A5):c.655G>A (p.Gly219Arg) rs144332569
NM_177550.4(SLC13A5):c.680C>T (p.Thr227Met) rs587777577
NM_182961.4(SYNE1):c.19692+3G>A rs150304757
NM_182961.4(SYNE1):c.21377A>G (p.Lys7126Arg) rs145882956
NM_182961.4(SYNE1):c.2818G>A (p.Glu940Lys) rs757479164
NM_198569.3(ADGRG6):c.19C>T (p.Arg7Ter) rs749355583
Single allele

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