ClinVar Miner

Variants from ClinPGx with conflicting interpretations

Location: United States  Primary collection method: curation
Minimum review status of the submission from ClinPGx: Collection method of the submission from ClinPGx:
Minimum review status of the other submission: Collection method of the other submission:
Minimum conflict level:

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
18 4 0 0 0 114 0 114

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
ClinPGx pathogenic likely pathogenic uncertain significance likely benign benign association other
drug response 75 36 23 17 29 1 4

Submitter to submitter summary #

Total submitters: 85
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
GeneDx 0 0 0 0 0 58 0 58
Labcorp Genetics (formerly Invitae), Labcorp 0 0 0 0 0 47 0 47
PreventionGenetics, part of Exact Sciences 0 0 0 0 0 43 0 43
CeGaT Center for Human Genetics Tuebingen 0 0 0 0 0 40 0 40
ClinGen Malignant Hyperthermia Susceptibility Variant Curation Expert Panel, ClinGen 0 0 0 0 0 36 0 36
Revvity Omics, Revvity 0 0 0 0 0 31 0 31
Eurofins Ntd Llc (ga) 0 0 0 0 0 29 0 29
Quest Diagnostics Nichols Institute San Juan Capistrano 0 0 0 0 0 23 0 23
Mayo Clinic Laboratories, Mayo Clinic 0 0 0 0 0 20 0 20
All of Us Research Program, National Institutes of Health 0 0 0 0 0 19 0 19
OMIM 0 2 0 0 0 19 0 19
Color Diagnostics, LLC DBA Color Health 0 0 0 0 0 18 0 18
Dasa 0 0 0 0 0 16 0 16
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories 0 0 0 0 0 13 0 13
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen 0 0 0 0 0 12 0 12
Fulgent Genetics, Fulgent Genetics 0 0 0 0 0 12 0 12
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ 0 0 0 0 0 11 0 11
Athena Diagnostics 0 0 0 0 0 10 0 10
AiLife Diagnostics, AiLife Diagnostics 0 0 0 0 0 9 0 9
Clinical Genetics Laboratory, Skane University Hospital Lund 0 0 0 0 0 9 0 9
Institute of Human Genetics, University of Leipzig Medical Center 0 0 0 0 0 9 0 9
Variantyx, Inc. 0 0 0 0 0 9 0 9
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 0 0 0 0 0 9 0 9
Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics 0 0 0 0 0 8 0 8
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center 0 0 0 0 0 7 0 7
Department of Pathology and Laboratory Medicine, Sinai Health System 0 0 0 0 0 6 0 6
Laboratory of Genetics, Children's Clinical University Hospital Latvia 0 0 0 0 0 6 0 6
Clinical Genetics and Genomics, Karolinska University Hospital 0 0 0 0 0 5 0 5
Genome Diagnostics Laboratory, Amsterdam University Medical Center 0 0 0 0 0 5 0 5
Genome Diagnostics Laboratory, University Medical Center Utrecht 0 0 0 0 0 5 0 5
Genetic Services Laboratory, University of Chicago 0 0 0 0 0 4 0 4
Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center 0 0 0 0 0 4 0 4
HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas 0 0 0 0 0 4 0 4
HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology 0 0 0 0 0 4 0 4
Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine 0 0 0 0 0 4 0 4
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen 0 0 0 0 0 4 0 4
Institute of Reproductive Genetics, University of Münster 0 0 0 0 0 4 0 4
Juno Genomics, Hangzhou Juno Genomics, Inc 0 0 0 0 0 4 0 4
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine 0 2 0 0 0 4 0 4
Mendelics 0 0 0 0 0 4 0 4
NHS Central & South Genomic Laboratory Hub 0 0 0 0 0 4 0 4
Daryl Scott Lab, Baylor College of Medicine 0 0 0 0 0 3 0 3
Genomic Research Center, Shahid Beheshti University of Medical Sciences 0 0 0 0 0 3 0 3
Institute of Immunology and Genetics Kaiserslautern 0 0 0 0 0 3 0 3
MGZ Medical Genetics Center 0 0 0 0 0 3 0 3
Molecular Genetics, Royal Melbourne Hospital 0 0 0 0 0 3 0 3
New York Genome Center 0 0 0 0 0 3 0 3
Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego 0 0 0 0 0 3 0 3
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute 0 0 0 0 0 3 0 3
Blueprint Genetics 0 0 0 0 0 2 0 2
Breakthrough Genomics, Breakthrough Genomics 0 0 0 0 0 2 0 2
CSER _CC_NCGL, University of Washington 0 0 0 0 0 2 0 2
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital 0 0 0 0 0 2 0 2
Clinical Genomics Laboratory, Washington University in St. Louis 0 0 0 0 0 2 0 2
Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden 0 0 0 0 0 2 0 2
Institute of Human Genetics Munich, TUM University Hospital 0 0 0 0 0 2 0 2
Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein 0 0 0 0 0 2 0 2
3billion 0 0 0 0 0 1 0 1
Baylor Genetics 0 0 0 0 0 1 0 1
Biesecker Lab/Clinical Genomics Section, National Institutes of Health 0 0 0 0 0 1 0 1
Center for Personalized Medicine, Children's Hospital Los Angeles 0 0 0 0 0 1 0 1
Centre for Clinical Genetics and Genomic Diagnostics, Zealand University Hospital 0 0 0 0 0 1 0 1
Centre for Mendelian Genomics, University Medical Centre Ljubljana 0 0 0 0 0 1 0 1
Clinical Genetics, Academic Medical Center 0 0 0 0 0 1 0 1
Clinical Genomic Analysis (GENYSIS) Core, University of North Carolina at Chapel Hill 0 0 0 0 0 1 0 1
Department of Genetics, Reproduction and Fetal Medicine., Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville. 0 0 0 0 0 1 0 1
Department of Genetics, Rouen University Hospital, Normandy Center for Genomic and Personalized Medicine 0 0 0 0 0 1 0 1
Department of Human Genetics, Hannover Medical School 0 0 0 0 0 1 0 1
Department of Pharmacology - Sarajevo Medical School, University Sarajevo School of Science and Technology 0 0 0 0 0 1 0 1
Division of Medical Genetics, University of Washington 0 0 0 0 0 1 0 1
Dubai Health Genomic Medicine Center, Dubai Health 0 0 0 0 0 1 0 1
Equipe Genetique des Anomalies du Developpement, Université de Bourgogne 0 0 0 0 0 1 0 1
Genetics Laboratory, Great Ormond Street Hospital NHS Foundation Trust, North Thames Genomic Laboratory Hub 0 0 0 0 0 1 0 1
Genetics and Molecular Pathology, SA Pathology 0 0 0 0 0 1 0 1
Gharavi Laboratory, Columbia University 0 0 0 0 0 1 0 1
Hadassah Hebrew University Medical Center 0 0 0 0 0 1 0 1
Illumina Laboratory Services, Illumina 0 0 0 0 0 1 0 1
Institute of Human Genetics, Clinical Exome/Genome Diagnostics Group, University Hospital Bonn 0 0 0 0 0 1 0 1
Kariminejad - Najmabadi Pathology & Genetics Center 0 0 0 0 0 1 0 1
Laboratory of Medical Genetics, National & Kapodistrian University of Athens 0 0 0 0 0 1 0 1
Laboratory of Molecular Genetics (Pr. Bezieau's lab), CHU de Nantes 0 0 0 0 0 1 0 1
Molecular Diagnostic Laboratory for Inherited Cardiovascular Disease, Montreal Heart Institute 0 0 0 0 0 1 0 1
Pittsburgh Clinical Genomics Laboratory, University of Pittsburgh Medical Center 0 0 0 0 0 1 0 1
Stanford Center for Inherited Cardiovascular Disease, Stanford University 0 0 0 0 0 1 0 1
deCODE genetics, Amgen 0 0 0 0 0 1 0 1

All variants with conflicting interpretations #

Total variants: 114
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HGVS dbSNP gnomAD frequency
NM_006297.3(XRCC1):c.1196A>G (p.Gln399Arg) rs25487 0.71503
NM_024006.6(VKORC1):c.283+837T>C rs2359612 0.65429
NM_194255.4(SLC19A1):c.80A>G (p.His27Arg) rs1051266 0.51696
NM_024006.6(VKORC1):c.*134G>A rs7294 0.39850
NC_000019.10:g.39248147C>T rs12979860 0.37827
NM_024006.4(VKORC1):c.-1639G>A rs9923231 0.31727
NM_024006.6(VKORC1):c.174-136C>T rs9934438 0.31147
NM_000767.5(CYP2B6):c.516G>T (p.Gln172His) rs3745274 0.28231
NM_000110.4(DPYD):c.85T>C (p.Cys29Arg) rs1801265 0.27966
NM_004044.7(ATIC):c.1503+675T>C rs4673993 0.25749
NM_000745.4(CHRNA5):c.1192G>A (p.Asp398Asn) rs16969968 0.23879
NM_001082.5(CYP4F2):c.1297G>A (p.Val433Met) rs2108622 0.22897
NM_000110.4(DPYD):c.1627A>G (p.Ile543Val) rs1801159 0.18640
NM_001354761.2(ADD1):c.1378G>T (p.Gly460Trp) rs4961 0.16822
NC_000019.10:g.39252525T>G rs8099917 0.15536
NC_000006.12:g.31575254G>A rs1800629 0.13769
NM_006446.5(SLCO1B1):c.521T>C (p.Val174Ala) rs4149056 0.12106
NM_033453.4(ITPA):c.124+21A>C rs7270101 0.09874
NM_004827.3(ABCG2):c.421C>A (p.Gln141Lys) rs2231142 0.09384
NM_000110.4(DPYD):c.496A>G (p.Met166Val) rs2297595 0.08071
NM_000041.2(APOE):c.526C>T (p.Arg176Cys) rs7412 0.07986
NM_033453.4(ITPA):c.94C>A (p.Pro32Thr) rs1127354 0.06104
NM_000110.4(DPYD):c.1896T>C (p.Phe632=) rs17376848 0.04333
NM_000110.4(DPYD):c.2194G>A (p.Val732Ile) rs1801160 0.03993
NM_000767.5(CYP2B6):c.983T>C (p.Ile328Thr) rs28399499 0.02197
NM_000130.4(F5):c.1601G>A (p.Arg534Gln) rs6025 0.01762
NM_000110.4(DPYD):c.1601G>A (p.Ser534Asn) rs1801158 0.01373
NM_000110.4(DPYD):c.1236G>A (p.Glu412=) rs56038477 0.01305
NM_000110.4(DPYD):c.1129-5923C>G rs75017182 0.01296
NM_001025195.2(CES1):c.431G>A (p.Gly144Glu) rs71647871 0.00998
NM_018283.4(NUDT15):c.415C>T (p.Arg139Cys) rs116855232 0.00927
NM_000690.4(ALDH2):c.1510G>A (p.Glu504Lys) rs671 0.00596
NM_000110.4(DPYD):c.557A>G (p.Tyr186Cys) rs115232898 0.00585
NM_000110.4(DPYD):c.1905+1G>A rs3918290 0.00474
NM_000492.4(CFTR):c.220C>T (p.Arg74Trp) rs115545701 0.00350
NM_000110.4(DPYD):c.2846A>T (p.Asp949Val) rs67376798 0.00334
NM_024006.6(VKORC1):c.106G>T (p.Asp36Tyr) rs61742245 0.00150
NM_000110.4(DPYD):c.1679T>G (p.Ile560Ser) rs55886062 0.00040
NM_000492.4(CFTR):c.3154T>G (p.Phe1052Val) rs150212784 0.00037
NM_000492.4(CFTR):c.3454G>C (p.Asp1152His) rs75541969 0.00033
NM_000492.4(CFTR):c.3209G>A (p.Arg1070Gln) rs78769542 0.00030
NM_000492.4(CFTR):c.1652G>A (p.Gly551Asp) rs75527207 0.00022
NM_000492.4(CFTR):c.617T>G (p.Leu206Trp) rs121908752 0.00013
NM_000110.4(DPYD):c.2303C>A (p.Thr768Lys) rs56005131 0.00011
NM_000540.3(RYR1):c.1840C>T (p.Arg614Cys) rs118192172 0.00011
NM_000110.4(DPYD):c.1774C>T (p.Arg592Trp) rs59086055 0.00006
NM_000492.4(CFTR):c.1646G>A (p.Ser549Asn) rs121908755 0.00006
NM_000540.3(RYR1):c.7300G>A (p.Gly2434Arg) rs121918593 0.00005
NM_005228.5(EGFR):c.2369C>T (p.Thr790Met) rs121434569 0.00005
NM_000492.4(CFTR):c.2834C>T (p.Ser945Leu) rs397508442 0.00004
NM_000492.4(CFTR):c.200C>T (p.Pro67Leu) rs368505753 0.00003
NM_000492.4(CFTR):c.3208C>T (p.Arg1070Trp) rs202179988 0.00003
NM_000069.3(CACNA1S):c.520C>T (p.Arg174Trp) rs772226819 0.00002
NM_000492.4(CFTR):c.1055G>A (p.Arg352Gln) rs121908753 0.00002
NM_000492.4(CFTR):c.328G>C (p.Asp110His) rs113993958 0.00002
NM_000492.4(CFTR):c.330C>A (p.Asp110Glu) rs397508537 0.00002
NM_000492.4(CFTR):c.532G>A (p.Gly178Arg) rs80282562 0.00002
NM_000540.3(RYR1):c.1201C>T (p.Arg401Cys) rs193922764 0.00002
NM_000492.4(CFTR):c.1647T>G (p.Ser549Arg) rs121909005 0.00001
NM_000492.4(CFTR):c.166G>A (p.Glu56Lys) rs397508256 0.00001
NM_000492.4(CFTR):c.2930C>T (p.Ser977Phe) rs141033578 0.00001
NM_000492.4(CFTR):c.3222T>A (p.Phe1074Leu) rs186045772 0.00001
NM_000492.4(CFTR):c.3731G>A (p.Gly1244Glu) rs267606723 0.00001
NM_000492.4(CFTR):c.3752G>A (p.Ser1251Asn) rs74503330 0.00001
NM_000540.3(RYR1):c.103T>C (p.Cys35Arg) rs193922747 0.00001
NM_000540.3(RYR1):c.14545G>A (p.Val4849Ile) rs118192168 0.00001
NM_000540.3(RYR1):c.1597C>T (p.Arg533Cys) rs193922768 0.00001
NM_000540.3(RYR1):c.6487C>T (p.Arg2163Cys) rs118192175 0.00001
NM_000540.3(RYR1):c.7007G>A (p.Arg2336His) rs112563513 0.00001
NM_000540.3(RYR1):c.7063C>T (p.Arg2355Trp) rs193922803 0.00001
NM_000540.3(RYR1):c.7282G>A (p.Ala2428Thr) rs193922809 0.00001
NM_000540.3(RYR1):c.7360C>T (p.Arg2454Cys) rs193922816 0.00001
NM_000540.3(RYR1):c.7361G>A (p.Arg2454His) rs118192122 0.00001
NM_000540.3(RYR1):c.7372C>T (p.Arg2458Cys) rs28933397 0.00001
NM_000540.3(RYR1):c.7373G>A (p.Arg2458His) rs121918594 0.00001
NC_012920.1(MT-RNR1):m.1095T>C rs267606618
NC_012920.1(MT-RNR1):m.1494C>T rs267606619
NC_012920.1(MT-RNR1):m.1555A>G rs267606617
NM_000069.3(CACNA1S):c.3257G>A (p.Arg1086His) rs1800559
NM_000492.3(CFTR):c.1521_1523del (p.Phe508del) rs113993960
NM_000492.4(CFTR):c.1364C>A (p.Ala455Glu) rs74551128
NM_000492.4(CFTR):c.1645A>C (p.Ser549Arg) rs121908757
NM_000492.4(CFTR):c.1651G>A (p.Gly551Ser) rs121909013
NM_000492.4(CFTR):c.1736A>G (p.Asp579Gly) rs397508288
NM_000492.4(CFTR):c.3199G>A (p.Ala1067Thr) rs121909020
NM_000492.4(CFTR):c.349C>T (p.Arg117Cys) rs77834169
NM_000492.4(CFTR):c.350G>A (p.Arg117His) rs78655421
NM_000540.3(RYR1):c.11969G>T (p.Gly3990Val) rs193922843
NM_000540.3(RYR1):c.1209C>G (p.Ile403Met) rs118192116
NM_000540.3(RYR1):c.130C>T (p.Arg44Cys) rs193922748
NM_000540.3(RYR1):c.14387A>G (p.Tyr4796Cys) rs118192167
NM_000540.3(RYR1):c.14477C>T (p.Thr4826Ile) rs121918595
NM_000540.3(RYR1):c.14497C>T (p.His4833Tyr) rs193922876
NM_000540.3(RYR1):c.14512C>G (p.Leu4838Val) rs193922878
NM_000540.3(RYR1):c.14582G>A (p.Arg4861His) rs63749869
NM_000540.3(RYR1):c.14693T>C (p.Ile4898Thr) rs118192170
NM_000540.3(RYR1):c.1565A>C (p.Tyr522Ser) rs118192162
NM_000540.3(RYR1):c.1654C>T (p.Arg552Trp) rs193922770
NM_000540.3(RYR1):c.1841G>T (p.Arg614Leu) rs193922772
NM_000540.3(RYR1):c.487C>T (p.Arg163Cys) rs118192161
NM_000540.3(RYR1):c.488G>T (p.Arg163Leu) rs193922753
NM_000540.3(RYR1):c.6488G>A (p.Arg2163His) rs118192163
NM_000540.3(RYR1):c.6502G>A (p.Val2168Met) rs118192176
NM_000540.3(RYR1):c.7039GAG[1] (p.Glu2348del) rs121918596
NM_000540.3(RYR1):c.7048G>A (p.Ala2350Thr) rs193922802
NM_000540.3(RYR1):c.7124G>C (p.Gly2375Ala) rs193922807
NM_000540.3(RYR1):c.7304G>A (p.Arg2435His) rs28933396
NM_000540.3(RYR1):c.7354C>T (p.Arg2452Trp) rs118192124
NM_000540.3(RYR1):c.7523G>A (p.Arg2508His) rs193922818
NM_000540.3(RYR1):c.9310G>A (p.Glu3104Lys) rs193922832
NM_000540.3(RYR1):c.982C>T (p.Arg328Trp) rs193922762
NM_000789.4(ACE):c.2306-105_2306-104insTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCATACAGTCACTTTT rs1799752
NM_001430.5(EPAS1):c.1035-7C>G rs7557402
NM_024006.6(VKORC1):c.283+124G>C rs8050894

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