ClinVar Miner

Variants from PharmGKB with conflicting interpretations

Location: United States — Primary collection method: curation
Minimum review status of the submission from PharmGKB: Collection method of the submission from PharmGKB:
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
75 53 0 0 0 120 0 120

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
PharmGKB pathogenic likely pathogenic uncertain significance likely benign benign association protective risk factor other
drug response 62 18 15 13 34 2 1 11 12

Submitter to submitter summary #

Total submitters: 35
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 47 0 47
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics 0 0 0 0 0 39 0 39
PreventionGenetics, PreventionGenetics 0 0 0 0 0 33 0 33
Invitae 0 0 0 0 0 29 0 29
OMIM 0 7 0 0 0 25 0 25
CeGaT Praxis fuer Humangenetik Tuebingen 0 0 0 0 0 21 0 21
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories 0 0 0 0 0 19 0 19
Quest Diagnostics Nichols Institute San Juan Capistrano 0 0 0 0 0 19 0 19
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics 0 0 0 0 0 12 0 12
Laboratory for Molecular Medicine,Partners HealthCare Personalized Medicine 0 2 0 0 0 8 0 8
Integrated Genetics/Laboratory Corporation of America 0 0 0 0 0 8 0 8
Department of Pathology and Laboratory Medicine,Sinai Health System 0 0 0 0 0 7 0 7
Genetic Services Laboratory, University of Chicago 0 0 0 0 0 4 0 4
Clinical Genetics Karolinska University Hospital,Karolinska University Hospital 0 0 0 0 0 4 0 4
Natera, Inc. 0 0 0 0 0 3 0 3
Blueprint Genetics 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
Illumina Clinical Services Laboratory,Illumina 0 0 0 0 0 3 0 3
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen 0 0 0 0 0 3 0 3
Athena Diagnostics Inc 0 0 0 0 0 2 0 2
CFTR-France 0 0 0 0 0 2 0 2
Greenwood Genetic Center Diagnostic Laboratories,Greenwood Genetic Center 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
Claritas Genomics 0 0 0 0 0 1 0 1
FirmaLab,FirmaLab 0 0 0 0 0 1 0 1
Mayo Clinic Laboratories, Mayo Clinic 0 0 0 0 0 1 0 1
Stanford Center for Inherited Cardiovascular Disease, Stanford University 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
Centre for Mendelian Genomics,University Medical Centre Ljubljana 0 0 0 0 0 1 0 1
Institute of Human Genetics, University of Leipzig Medical Center 0 0 0 0 0 1 0 1
CHLA Center for Personalized Medicine,Children's Hospital, Los Angeles 0 0 0 0 0 1 0 1
Broad Institute Rare Disease Group, Broad Institute 0 0 0 0 0 1 0 1
Gharavi Laboratory,Columbia University 0 0 0 0 0 1 0 1
HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas 0 0 0 0 0 1 0 1

All variants with conflicting interpretations #

Total variants: 120
Download table as spreadsheet
HGVS dbSNP
CYP2C19*3 rs4986893
CYP2C19*4A rs28399504
CYP2C9*2 rs1799853
CYP2C9*3 rs1057910
CYP2C9*5 rs28371686
CYP2D6*4 rs3892097
NC_000019.9:g.39743165T>G rs8099917
NC_012920.1:m.1494C>T rs267606619
NC_012920.1:m.1555A>G rs267606617
NM_000041.2(APOE):c.526C>T (p.Arg176Cys) rs7412
NM_000069.3(CACNA1S):c.520C>T (p.Arg174Trp) rs772226819
NM_000110.4(DPYD):c.1679T>G (p.Ile560Ser) rs55886062
NM_000110.4(DPYD):c.1905+1G>A rs3918290
NM_000110.4(DPYD):c.2846A>T (p.Asp949Val) rs67376798
NM_000120.4(EPHX1):c.337T>C (p.Tyr113His) rs1051740
NM_000120.4(EPHX1):c.416A>G (p.His139Arg) rs2234922
NM_000130.5(F5):c.1601= (p.Arg534=) rs6025
NM_000173.7(GP1BA):c.482C>T (p.Thr161Met) rs6065
NM_000373.4(UMPS):c.638G>C (p.Gly213Ala) rs1801019
NM_000376.3(VDR):c.2T>C (p.Met1Thr) rs2228570
NM_000402.4(G6PD):c.292G>A (p.Val98Met) rs1050828
NM_000492.3(CFTR):c.1521_1523delCTT (p.Phe508delPhe) rs113993960
NM_000492.4(CFTR):c.1040G>A (p.Arg347His) rs77932196
NM_000492.4(CFTR):c.1055G>A (p.Arg352Gln) rs121908753
NM_000492.4(CFTR):c.1624G>T (p.Gly542Ter) rs113993959
NM_000492.4(CFTR):c.1645A>C (p.Ser549Arg) rs121908757
NM_000492.4(CFTR):c.1646G>A (p.Ser549Asn) rs121908755
NM_000492.4(CFTR):c.1647T>G (p.Ser549Arg) rs121909005
NM_000492.4(CFTR):c.1651G>A (p.Gly551Ser) rs121909013
NM_000492.4(CFTR):c.1652G>A (p.Gly551Asp) rs75527207
NM_000492.4(CFTR):c.200C>T (p.Pro67Leu) rs368505753
NM_000492.4(CFTR):c.220C>T (p.Arg74Trp) rs115545701
NM_000492.4(CFTR):c.2834C>T (p.Ser945Leu) rs397508442
NM_000492.4(CFTR):c.2930C>T (p.Ser977Phe) rs141033578
NM_000492.4(CFTR):c.3154T>G (p.Phe1052Val) rs150212784
NM_000492.4(CFTR):c.3199G>A (p.Ala1067Thr) rs121909020
NM_000492.4(CFTR):c.3208C>T (p.Arg1070Trp) rs202179988
NM_000492.4(CFTR):c.3209G>A (p.Arg1070Gln) rs78769542
NM_000492.4(CFTR):c.3222T>A (p.Phe1074Leu) rs186045772
NM_000492.4(CFTR):c.328G>C (p.Asp110His) rs113993958
NM_000492.4(CFTR):c.330C>A (p.Asp110Glu) rs397508537
NM_000492.4(CFTR):c.3454G>C (p.Asp1152His) rs75541969
NM_000492.4(CFTR):c.350G>A (p.Arg117His) rs78655421
NM_000492.4(CFTR):c.3752G>A (p.Ser1251Asn) rs74503330
NM_000492.4(CFTR):c.3808G>A (p.Asp1270Asn) rs11971167
NM_000492.4(CFTR):c.3846G>A (p.Trp1282Ter) rs77010898
NM_000492.4(CFTR):c.532G>A (p.Gly178Arg) rs80282562
NM_000492.4(CFTR):c.617T>G (p.Leu206Trp) rs121908752
NM_000524.3(HTR1A):c.-1019G>C rs6295
NM_000525.3(KCNJ11):c.67A>G (p.Lys23Glu) rs5219
NM_000540.3(RYR1):c.1021G>A (p.Gly341Arg) rs121918592
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.14545G>A (p.Val4849Ile) rs118192168
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.1589G>A (p.Arg530His) rs111888148
NM_000540.3(RYR1):c.1598G>A (p.Arg533His) rs144336148
NM_000540.3(RYR1):c.1654C>T (p.Arg552Trp) rs193922770
NM_000540.3(RYR1):c.1840C>T (p.Arg614Cys) rs118192172
NM_000540.3(RYR1):c.487C>T (p.Arg163Cys) rs118192161
NM_000540.3(RYR1):c.6487C>T (p.Arg2163Cys) rs118192175
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.7007G>A (p.Arg2336His) rs112563513
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.7063C>T (p.Arg2355Trp) rs193922803
NM_000540.3(RYR1):c.7282G>A (p.Ala2428Thr) rs193922809
NM_000540.3(RYR1):c.7300G>A (p.Gly2434Arg) rs121918593
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.7360C>T (p.Arg2454Cys) rs193922816
NM_000540.3(RYR1):c.7361G>A (p.Arg2454His) rs118192122
NM_000540.3(RYR1):c.7372C>T (p.Arg2458Cys) rs28933397
NM_000540.3(RYR1):c.7373G>A (p.Arg2458His) rs121918594
NM_000540.3(RYR1):c.742G>A (p.Gly248Arg) rs1801086
NM_000540.3(RYR1):c.7522C>G (p.Arg2508Gly) rs118192178
NM_000540.3(RYR1):c.7523G>A (p.Arg2508His) rs193922818
NM_000540.3(RYR1):c.9310G>A (p.Glu3104Lys) rs193922832
NM_000546.6(TP53):c.215C>G (p.Pro72Arg) rs1042522
NM_000594.3(TNF):c.-488G>A rs1800629
NM_000621.4(HTR2A):c.614-2211T>C rs7997012
NM_000636.4(SOD2):c.47T>C (p.Val16Ala) rs4880
NM_000743.5(CHRNA3):c.645C>T (p.Tyr215=) rs1051730
NM_000745.3(CHRNA5):c.1192G>A (p.Asp398Asn) rs16969968
NM_000754.4(COMT):c.472G>A (p.Val158Met) rs4680
NM_000769.1(CYP2C19):c.681G>A (p.Pro227=) rs4244285
NM_000777.5(CYP3A5):c.219-237= rs776746
NM_000795.3(DRD2):c.-585A>G rs1799978
NM_000868.3(HTR2C):c.551-3008C>G rs1414334
NM_000903.3(NQO1):c.559C>T (p.Pro187Ser) rs1800566
NM_001025195.2(CES1):c.431G>A (p.Gly144Glu) rs71647871
NM_001119.5(ADD1):c.1378G>T (p.Gly460Trp) rs4961
NM_001127593.1(FCGR3A):c.526T>G (p.Phe176Val) rs396991
NM_001136219.3(FCGR2A):c.500A>G (p.His167Arg) rs1801274
NM_001146274.2(TCF7L2):c.450+33966C>T rs7903146
NM_001276254.2(IFNL4):c.151-152G>A rs12979860
NM_001348946.2(ABCB1):c.2677T>G (p.Ser893Ala) rs2032582
NM_001348946.2(ABCB1):c.3435T>C (p.Ile1145=) rs1045642
NM_002075.4(GNB3):c.825C>T (p.Ser275=) rs5443
NM_002454.3(MTRR):c.66A>G (p.Ile22Met) rs1801394
NM_004628.5(XPC):c.2815C>A (p.Gln939Lys) rs2228001
NM_004827.3(ABCG2):c.421C>A (p.Gln141Lys) rs2231142
NM_004985.5(KRAS):c.38G>T (p.Gly13Val) rs112445441
NM_005228.5(EGFR):c.2369C>T (p.Thr790Met) rs121434569
NM_005577.4(LPA):c.3947+467T>C rs10455872
NM_005957.5(MTHFR):c.665C>T (p.Ala222Val) rs1801133
NM_006440.5(TXNRD2):c.103+197G>A rs13306278
NM_006446.5(SLCO1B1):c.521T>C (p.Val174Ala) rs4149056
NM_014619.5(GRIK4):c.83-10039T>C rs1954787
NM_017460.5(CYP3A4):c.-392G>A rs2740574
NM_024006.6(VKORC1):c.173+525C>T rs17708472
NM_024006.6(VKORC1):c.174-136C>T rs9934438
NM_024006.6(VKORC1):c.283+124G>C rs8050894
NM_024006.6(VKORC1):c.283+837T>C rs2359612
NM_178510.2(ANKK1):c.2137G>A (p.Glu713Lys) rs1800497
UGT1A1*6 rs4148323
m.1095T>C rs267606618

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