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 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
68 45 0 0 0 135 0 135

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 affects association protective risk factor other
drug response 77 32 22 14 32 3 2 1 27 13

Submitter to submitter summary #

Total submitters: 53
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 13 0 0 0 68 0 68
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics 0 0 0 0 0 39 0 39
GeneDx 0 0 0 0 0 35 0 35
PreventionGenetics 0 0 0 0 0 33 0 33
Invitae 0 0 0 0 0 33 0 33
Counsyl 0 0 0 0 0 31 0 31
Integrated Genetics/Laboratory Corporation of America 0 0 0 0 0 30 0 30
Illumina Clinical Services Laboratory,Illumina 0 0 0 0 0 24 0 24
CFTR2 0 0 0 0 0 21 0 21
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories 0 0 0 0 0 17 0 17
Mendelics 0 0 0 0 0 17 0 17
Quest Diagnostics Nichols Institute San Juan Capistrano 0 0 0 0 0 17 0 17
Laboratory for Molecular Medicine,Partners HealthCare Personalized Medicine 0 1 0 0 0 16 0 16
GeneReviews 0 0 0 0 0 12 0 12
Fulgent Genetics 0 0 0 0 0 12 0 12
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics 0 0 0 0 0 12 0 12
HudsonAlpha Institute for Biotechnology 0 0 0 0 0 7 0 7
Genetic Services Laboratory, University of Chicago 0 0 0 0 0 6 0 6
American College of Medical Genetics and Genomics (ACMG) 0 0 0 0 0 6 0 6
Ambry Genetics 0 0 0 0 0 5 0 5
CSER_CC_NCGL; University of Washington Medical Center 0 0 0 0 0 4 0 4
Division of Human Genetics,Children's Hospital of Philadelphia 0 0 0 0 0 4 0 4
Department of Genetics,Sultan Qaboos University Hospital, Oman 0 0 0 0 0 4 0 4
Human Genome Sequencing Center Clinical Lab,Baylor College of Medicine 0 0 0 0 0 3 0 3
Knight Diagnostic Laboratories,Oregon Health and Sciences University 0 0 0 0 0 3 0 3
Database of Curated Mutations (DoCM) 0 5 0 0 0 3 0 3
Diagnostic Laboratory, Department of Genetics,University Medical Center Groningen 0 0 0 0 0 3 0 3
Athena Diagnostics Inc 0 0 0 0 0 2 0 2
Biesecker Lab/Human Development Section,National Institutes of Health 0 0 0 0 0 2 0 2
Institute of Human Genetics,Klinikum rechts der Isar 0 0 0 0 0 2 0 2
Department of Pharmacy and Biotechnology,University of Bologna 0 0 0 0 0 2 0 2
Equipe Genetique des Anomalies du Developpement,Université de Bourgogne 0 0 0 0 0 2 0 2
DNA and Cytogenetics Diagnostics Unit,Erasmus Medical Center 0 0 0 0 0 2 0 2
Claritas Genomics 0 0 0 0 0 1 0 1
FirmaLab 0 0 0 0 0 1 0 1
Genome Diagnostics Laboratory,University Medical Center Utrecht 0 0 0 0 0 1 0 1
Courtagen Diagnostics Laboratory,Courtagen Life Sciences 0 0 0 0 0 1 0 1
Mayo Clinic Genetic Testing Laboratories,Mayo Clinic 0 0 0 0 0 1 0 1
Pathway Genomics 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
Stanford Center for Inherited Cardiovascular Disease,Stanford University 0 0 0 0 0 1 0 1
Center of Genomic medicine, Geneva,University Hospital of Geneva 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
Color 0 0 0 0 0 1 0 1
Donald Williams Parsons Laboratory,Baylor College of Medicine 0 0 0 0 0 1 0 1
Institute of Human Genetics,University of Wuerzburg 0 0 0 0 0 1 0 1
Centre for Mendelian Genomics,University Medical Centre Ljubljana 0 0 0 0 0 1 0 1
IntelligeneCG 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
Center for Precision Medicine,Vanderbilt University Medical Center 0 0 0 0 0 1 0 1
Molecular Diagnostics Laboratory,M Health: University of Minnesota 0 0 0 0 0 1 0 1
Gharavi Laboratory,Columbia University 0 0 0 0 0 1 0 1
Johns Hopkins Genomics,Johns Hopkins University 0 0 0 0 0 1 0 1

All variants with conflicting interpretations #

Total variants: 135
Download table as spreadsheet
HGVS dbSNP
NC_012920.1:m.1555A>G rs267606617
NG_011564.1:g.6399C>T rs9934438
NM_000041.2(APOE):c.526C>T (p.Arg176Cys) rs7412
NM_000069.3(CACNA1S):c.520C>T (p.Arg174Trp) rs772226819
NM_000106.5(CYP2D6):c.506-1G>A rs3892097
NM_000110.3(DPYD):c.1679T>G (p.Ile560Ser) rs55886062
NM_000110.3(DPYD):c.1905+1G>A rs3918290
NM_000110.3(DPYD):c.2846A>T (p.Asp949Val) rs67376798
NM_000110.3(DPYD):c.299_302delTCAT (p.Phe100Serfs) rs72549309
NM_000110.3(DPYD):c.557A>G (p.Tyr186Cys) rs115232898
NM_000110.3(DPYD):c.703C>T (p.Arg235Trp) rs1801266
NM_000130.4(F5):c.1601G= (p.Arg534=) rs6025
NM_000173.6(GP1BA):c.482C>T (p.Thr161Met) rs6065
NM_000373.3(UMPS):c.638G>C (p.Gly213Ala) rs1801019
NM_000402.4(G6PD):c.292G>A (p.Val98Met) rs1050828
NM_000492.3(CFTR):c.1040G>A (p.Arg347His) rs77932196
NM_000492.3(CFTR):c.1055G>A (p.Arg352Gln) rs121908753
NM_000492.3(CFTR):c.1364C>A (p.Ala455Glu) rs74551128
NM_000492.3(CFTR):c.1521_1523delCTT (p.Phe508delPhe) rs113993960
NM_000492.3(CFTR):c.1624G>T (p.Gly542Ter) rs113993959
NM_000492.3(CFTR):c.1645A>C (p.Ser549Arg) rs121908757
NM_000492.3(CFTR):c.1646G>A (p.Ser549Asn) rs121908755
NM_000492.3(CFTR):c.1647T>G (p.Ser549Arg) rs121909005
NM_000492.3(CFTR):c.1651G>A (p.Gly551Ser) rs121909013
NM_000492.3(CFTR):c.1652G>A (p.Gly551Asp) rs75527207
NM_000492.3(CFTR):c.166G>A (p.Glu56Lys) rs397508256
NM_000492.3(CFTR):c.200C>T (p.Pro67Leu) rs368505753
NM_000492.3(CFTR):c.220C>T (p.Arg74Trp) rs115545701
NM_000492.3(CFTR):c.2834C>T (p.Ser945Leu) rs397508442
NM_000492.3(CFTR):c.2930C>T (p.Ser977Phe) rs141033578
NM_000492.3(CFTR):c.3154T>G (p.Phe1052Val) rs150212784
NM_000492.3(CFTR):c.3199G>A (p.Ala1067Thr) rs121909020
NM_000492.3(CFTR):c.3208C>T (p.Arg1070Trp) rs202179988
NM_000492.3(CFTR):c.3209G>A (p.Arg1070Gln) rs78769542
NM_000492.3(CFTR):c.3222T>A (p.Phe1074Leu) rs186045772
NM_000492.3(CFTR):c.328G>C (p.Asp110His) rs113993958
NM_000492.3(CFTR):c.330C>A (p.Asp110Glu) rs397508537
NM_000492.3(CFTR):c.3454G>C (p.Asp1152His) rs75541969
NM_000492.3(CFTR):c.350G>A (p.Arg117His) rs78655421
NM_000492.3(CFTR):c.3731G>A (p.Gly1244Glu) rs267606723
NM_000492.3(CFTR):c.3752G>A (p.Ser1251Asn) rs74503330
NM_000492.3(CFTR):c.3763T>C (p.Ser1255Pro) rs121909041
NM_000492.3(CFTR):c.3808G>A (p.Asp1270Asn) rs11971167
NM_000492.3(CFTR):c.3846G>A (p.Trp1282Ter) rs77010898
NM_000492.3(CFTR):c.4046G>A (p.Gly1349Asp) rs193922525
NM_000492.3(CFTR):c.532G>A (p.Gly178Arg) rs80282562
NM_000492.3(CFTR):c.577G>A (p.Glu193Lys) rs397508759
NM_000492.3(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_000540.2(RYR1):c.1021G>A (p.Gly341Arg) rs121918592
NM_000540.2(RYR1):c.1209C>G (p.Ile403Met) rs118192116
NM_000540.2(RYR1):c.130C>T (p.Arg44Cys) rs193922748
NM_000540.2(RYR1):c.14387A>G (p.Tyr4796Cys) rs118192167
NM_000540.2(RYR1):c.14477C>T (p.Thr4826Ile) rs121918595
NM_000540.2(RYR1):c.14545G>A (p.Val4849Ile) rs118192168
NM_000540.2(RYR1):c.14582G>A (p.Arg4861His) rs63749869
NM_000540.2(RYR1):c.14693T>C (p.Ile4898Thr) rs118192170
NM_000540.2(RYR1):c.1565A>C (p.Tyr522Ser) rs118192162
NM_000540.2(RYR1):c.1589G>A (p.Arg530His) rs111888148
NM_000540.2(RYR1):c.1597C>A (p.Arg533Ser) rs193922768
NM_000540.2(RYR1):c.1598G>A (p.Arg533His) rs144336148
NM_000540.2(RYR1):c.1654C>T (p.Arg552Trp) rs193922770
NM_000540.2(RYR1):c.1840C>T (p.Arg614Cys) rs118192172
NM_000540.2(RYR1):c.487C>T (p.Arg163Cys) rs118192161
NM_000540.2(RYR1):c.6487C>T (p.Arg2163Cys) rs118192175
NM_000540.2(RYR1):c.6488G>A (p.Arg2163His) rs118192163
NM_000540.2(RYR1):c.6502G>A (p.Val2168Met) rs118192176
NM_000540.2(RYR1):c.7007G>A (p.Arg2336His) rs112563513
NM_000540.2(RYR1):c.7042_7044delGAG (p.Glu2348del) rs121918596
NM_000540.2(RYR1):c.7048G>A (p.Ala2350Thr) rs193922802
NM_000540.2(RYR1):c.7063C>T (p.Arg2355Trp) rs193922803
NM_000540.2(RYR1):c.7300G>A (p.Gly2434Arg) rs121918593
NM_000540.2(RYR1):c.7304G>A (p.Arg2435His) rs28933396
NM_000540.2(RYR1):c.7354C>T (p.Arg2452Trp) rs118192124
NM_000540.2(RYR1):c.7360C>T (p.Arg2454Cys) rs193922816
NM_000540.2(RYR1):c.7361G>A (p.Arg2454His) rs118192122
NM_000540.2(RYR1):c.7372C>T (p.Arg2458Cys) rs28933397
NM_000540.2(RYR1):c.7373G>A (p.Arg2458His) rs121918594
NM_000540.2(RYR1):c.742G>A (p.Gly248Arg) rs1801086
NM_000540.2(RYR1):c.7522C>G (p.Arg2508Gly) rs118192178
NM_000540.2(RYR1):c.7523G>A (p.Arg2508His) rs193922818
NM_000540.2(RYR1):c.9310G>A (p.Glu3104Lys) rs193922832
NM_000546.5(TP53):c.215C>G (p.Pro72Arg) rs1042522
NM_000621.4(HTR2A):c.614-2211T>C rs7997012
NM_000745.3(CHRNA5):c.1192G>A (p.Asp398Asn) rs16969968
NM_000754.3(COMT):c.472G>A (p.Val158Met) rs4680
NM_000767.5(CYP2B6):c.785A>G (p.Lys262Arg) rs2279343
NM_000769.1(CYP2C19):c.1A>G (p.Met1Val) rs28399504
NM_000769.1(CYP2C19):c.636G>A (p.Trp212Ter) rs4986893
NM_000769.1(CYP2C19):c.681G>A (p.Pro227=) rs4244285
NM_000771.3(CYP2C9):c.1075A>C (p.Ile359Leu) rs1057910
NM_000771.3(CYP2C9):c.430C>T (p.Arg144Cys) rs1799853
NM_000771.4(CYP2C9):c.1080C>G (p.Asp360Glu) rs28371686
NM_000795.3(DRD2):c.-585A>G rs1799978
NM_000795.3(DRD2):c.811-83G>T rs1076560
NM_000868.3(HTR2C):c.551-3008C>G rs1414334
NM_000903.2(NQO1):c.559C>T (p.Pro187Ser) rs1800566
NM_000927.4(ABCB1):c.2677T>G (p.Ser893Ala) rs2032582
NM_000927.4(ABCB1):c.3435T>C (p.Ile1145=) rs1045642
NM_001008503.2(OPRM1):c.118A>G (p.Asn40Asp) rs1799971
NM_001017535.1(VDR):c.2T>C (p.Met1Thr) rs2228570
NM_001024465.2(SOD2):c.47T>C (p.Val16Ala) rs4880
NM_001127593.1(FCGR3A):c.526T>G (p.Phe176Val) rs396991
NM_001136018.3(EPHX1):c.337T>C (p.Tyr113His) rs1051740
NM_001136018.3(EPHX1):c.416A>G (p.His139Arg) rs2234922
NM_001166694.1(CHRNA3):c.645C>T (p.Tyr215=) rs1051730
NM_001276254.2(IFNL4):c.151-152G>A rs12979860
NM_001963.5(EGF):c.-382A>G rs4444903
NM_002454.2(MTRR):c.66A>G (p.Ile22Met) rs1801394
NM_004628.4(XPC):c.2815C>A (p.Gln939Lys) rs2228001
NM_004827.2(ABCG2):c.421C>A (p.Gln141Lys) rs2231142
NM_005228.4(EGFR):c.2369C>T (p.Thr790Met) rs121434569
NM_005228.4(EGFR):c.2573T>G (p.Leu858Arg) rs121434568
NM_005957.4(MTHFR):c.665C>T (p.Ala222Val) rs1801133
NM_006446.4(SLCO1B1):c.521T>C (p.Val174Ala) rs4149056
NM_006920.4(SCN1A):c.603-91G>A rs3812718
NM_014619.4(GRIK4):c.83-10039T>C rs1954787
NM_017460.5(CYP3A4):c.-392G>A rs2740574
NM_021642.3(FCGR2A):c.497A>G (p.His166Arg) rs1801274
NM_024006.5(VKORC1):c.*134G>A rs7294
NM_024006.5(VKORC1):c.106G>T (p.Asp36Tyr) rs61742245
NM_024006.5(VKORC1):c.283+124G>C rs8050894
NM_025225.2(PNPLA3):c.444C>G (p.Ile148Met) rs738409
NM_030756.4(TCF7L2):c.382-41435C>T rs7903146
NM_031226.2(CYP19A1):c.*161T>G rs4646
NM_033360.3(KRAS):c.38G>T (p.Gly13Val) rs112445441
NM_033453.3(ITPA):c.124+21A>C rs7270101
NM_033453.3(ITPA):c.94C>A (p.Pro32Thr) rs1127354
NM_176801.2(ADD1):c.1378G>T (p.Gly460Trp) rs4961
NM_178510.1(ANKK1):c.2137G>A (p.Glu713Lys) rs1800497
NM_202001.2(ERCC1):c.354T>C (p.Asn118=) rs11615
UGT1A1*6 rs4148323
m.1095T>C rs267606618
m.1494C>T rs267606619

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