ClinVar Miner

Variants from GeneReviews with conflicting interpretations

Location: United States  Primary collection method: literature only
Minimum review status of the submission from GeneReviews: Collection method of the submission from GeneReviews:
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
2517 3585 1 93 8 3 56 146

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
GeneReviews pathogenic likely pathogenic uncertain significance likely benign benign other
pathogenic 1 88 41 13 10 0
likely pathogenic 1 0 0 0 0 0
uncertain significance 4 0 0 1 4 0
benign 1 1 3 4 0 1
association 0 0 0 1 1 0
other 1 0 0 0 0 0

Submitter to submitter summary #

Total submitters: 68
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
Labcorp Genetics (formerly Invitae), Labcorp 0 1175 0 10 3 1 27 41
Counsyl 0 206 0 18 0 0 7 25
Baylor Genetics 0 605 0 21 0 0 2 23
Fulgent Genetics, Fulgent Genetics 0 503 0 17 0 0 5 22
Illumina Laboratory Services, Illumina 0 433 0 3 4 1 10 18
Natera, Inc. 0 623 0 11 0 0 2 13
Mendelics 0 228 0 1 0 0 11 12
3billion 0 405 0 7 1 0 3 11
OMIM 0 1890 1 0 0 1 6 8
Revvity Omics, Revvity 0 283 0 7 0 0 1 8
Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard 0 143 0 5 0 0 2 7
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 0 593 0 7 0 0 0 7
Department of Pathology and Laboratory Medicine, Sinai Health System 0 143 0 1 0 0 5 6
Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India 0 49 0 4 0 0 1 5
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute 0 293 0 3 0 0 2 5
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories 0 105 0 1 0 1 2 4
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen 0 48 0 0 0 0 4 4
Ambry Genetics 0 38 0 1 0 1 1 3
CSER _CC_NCGL, University of Washington 0 5 0 0 0 0 3 3
Centre for Mendelian Genomics, University Medical Centre Ljubljana 0 71 0 2 0 0 1 3
Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre 0 169 0 1 0 0 2 3
Institute of Medical Molecular Genetics, University of Zurich 0 3 0 3 0 0 0 3
Laboratory of Molecular Genetics, CHU Rennes 0 4 0 3 0 0 0 3
MGZ Medical Genetics Center 0 107 0 2 0 0 1 3
Molecular Genetics, Royal Melbourne Hospital 0 34 0 0 0 0 3 3
Solve-RD Consortium 0 28 0 2 0 0 1 3
Variantyx, Inc. 0 108 0 3 0 0 0 3
Genetic Services Laboratory, University of Chicago 0 100 0 1 0 0 1 2
Genome-Nilou Lab 0 263 0 1 0 0 1 2
Genomic Research Center, Shahid Beheshti University of Medical Sciences 0 56 0 1 0 0 1 2
Juno Genomics, Hangzhou Juno Genomics, Inc 0 90 0 2 0 0 0 2
Myriad Genetics, Inc. 0 257 0 2 0 0 0 2
New York Genome Center 0 39 0 1 0 0 1 2
Pars Genome Lab 0 1 0 0 0 0 2 2
Soonchunhyang University Bucheon Hospital, Soonchunhyang University Medical Center 0 17 0 1 0 0 1 2
American College of Medical Genetics and Genomics (ACMG) 0 24 0 0 0 1 0 1
Arcensus 0 3 0 1 0 0 0 1
Breda Genetics srl, Breda Genetics srl 0 5 0 0 0 0 1 1
Cardiovascular Research Group, Instituto Nacional de Saude Doutor Ricardo Jorge 0 0 0 0 0 0 1 1
CeGaT Center for Human Genetics Tuebingen 0 9 0 1 0 0 0 1
Cirak Lab, University Hospital Cologne 0 0 0 1 0 0 0 1
Clinical Biochemistry Laboratory, Health Services Laboratory 0 18 0 0 1 0 0 1
Daryl Scott Lab, Baylor College of Medicine 0 20 0 0 0 0 1 1
Department of Laboratory Medicine and Genetics, Trillium Health Partners Credit Valley Hospital 0 10 0 1 0 0 0 1
Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics 0 46 0 1 0 0 0 1
Fundacion Hipercolesterolemia Familiar 0 0 0 0 0 0 1 1
Geisinger Autism and Developmental Medicine Institute, Geisinger Health System 0 0 0 0 0 0 1 1
GeneDx 0 26 0 1 0 0 0 1
GenePathDx, GenePath diagnostics 0 3 0 0 0 0 1 1
Genome Diagnostics Laboratory, University Medical Center Utrecht 0 17 0 0 0 0 1 1
Genomics England Pilot Project, Genomics England 0 33 0 1 0 0 0 1
Groupe Hospitalier Pitie Salpetriere, Uf Genomique Du Developpement, Assistance Publique Hopitaux de Paris Sorbonne Université 0 2 0 1 0 0 0 1
Inherited Neuropathy Consortium 0 6 0 0 0 0 1 1
Inherited Neuropathy Consortium Ii, University Of Miami 0 23 0 0 0 0 1 1
Institute of Human Genetics Munich, TUM University Hospital 0 122 0 1 0 0 0 1
Institute of Human Genetics, Heidelberg University 0 28 0 1 0 0 0 1
Institute of Human Genetics, University of Leipzig Medical Center 0 229 0 1 0 0 0 1
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen 0 46 0 1 0 0 0 1
Institute of Tissue Medicine and Pathology, University of Bern 0 0 0 1 0 0 0 1
Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM) 0 13 0 1 0 0 0 1
Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein 0 83 0 1 0 0 0 1
Laboratory of Cyto-molecular Genetics, Department of Anatomy, All India Institute of Medical Sciences (AIIMS), New Delhi 0 2 0 1 0 0 0 1
Laboratory of Medical Genetics, National & Kapodistrian University of Athens 0 101 0 1 0 0 0 1
Medical and Scientific Branch, Hong Kong Genome Institute 0 32 0 1 0 0 0 1
Molecular Diagnostics Laboratory, M Health Fairview: University of Minnesota 0 11 0 1 0 0 0 1
Robarts Research Institute, Western University 0 0 0 1 0 0 0 1
SN ONGC Dept of Genetics and Molecular biology Vision Research Foundation 0 0 0 1 0 0 0 1
SingHealth Duke-NUS Institute of Precision Medicine 0 11 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 146
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_207352.4(CYP4V2):c.64C>G (p.Leu22Val) rs1055138 0.45965
NM_015272.5(RPGRIP1L):c.685G>A (p.Ala229Thr) rs61747071 0.04969
NM_198578.3(LRRK2):c.149A>G (p.His50Arg) rs2256408 0.03048
NM_000096.4(CP):c.1652C>T (p.Thr551Ile) rs61733458 0.02278
NM_000784.4(CYP27A1):c.1151C>T (p.Pro384Leu) rs41272687 0.01532
NM_000171.4(GLRA1):c.1108G>A (p.Gly370Ser) rs116474260 0.00908
NM_001008216.2(GALE):c.770A>G (p.Lys257Arg) rs28940884 0.00568
NR_001566.3(TERC):n.228G>A rs141686314 0.00451
NM_001363.5(DKC1):c.-142C>G rs199422241 0.00227
NM_000193.4(SHH):c.885C>T (p.Ser295=) rs549625672 0.00218
NM_001384732.1(CPLANE1):c.8050G>A (p.Ala2684Thr) rs111294855 0.00205
NM_001127701.1(SERPINA1):c.739C>T (p.Arg247Cys) rs28929470 0.00199
NM_000193.4(SHH):c.869G>A (p.Gly290Asp) rs104894047 0.00191
NM_000096.4(CP):c.2684G>C (p.Gly895Ala) rs139633388 0.00162
NM_198578.4(LRRK2):c.225G>A (p.Ala75=) rs75054132 0.00146
NR_003051.4(RMRP):n.72A>G rs199476103 0.00123
NM_001008216.2(GALE):c.956G>A (p.Gly319Glu) rs28940885 0.00115
NM_001267550.2(TTN):c.102271C>T (p.Arg34091Trp) rs140319117 0.00095
NM_007272.3(CTRC):c.217G>A (p.Ala73Thr) rs515726209 0.00067
NM_016042.4(EXOSC3):c.395A>C (p.Asp132Ala) rs141138948 0.00048
NM_001127701.1(SERPINA1):c.1159G>A (p.Glu387Lys) rs121912712 0.00042
NM_033629.6(TREX1):c.341G>A (p.Arg114His) rs72556554 0.00030
NM_025114.4(CEP290):c.2991+1655A>G rs281865192 0.00028
NM_001953.5(TYMP):c.622G>A (p.Val208Met) rs121913039 0.00027
NM_002055.5(GFAP):c.667G>C (p.Glu223Gln) rs56679084 0.00027
NM_207352.4(CYP4V2):c.367A>G (p.Met123Val) rs149684063 0.00027
NM_000096.4(CP):c.2158C>T (p.Arg720Trp) rs145784949 0.00023
NC_000002.12:g.189564177T>A rs368420430 0.00022
NM_198578.4(LRRK2):c.3960G>T (p.Arg1320Ser) rs77018758 0.00021
NM_001048174.2(MUTYH):c.1034C>T (p.Ala345Val) rs35352891 0.00020
NM_004004.6(GJB2):c.-23+1G>A rs80338940 0.00017
NM_000784.4(CYP27A1):c.1184G>A (p.Arg395His) rs587778778 0.00011
NM_001127701.1(SERPINA1):c.1178C>T (p.Pro393Leu) rs199422209 0.00011
NM_000784.4(CYP27A1):c.379C>T (p.Arg127Trp) rs201114717 0.00010
NM_001953.5(TYMP):c.665A>G (p.Lys222Arg) rs149977726 0.00010
NM_207352.4(CYP4V2):c.1198C>T (p.Arg400Cys) rs138444697 0.00009
NR_104387.1(TAF1):n.5894C>T rs397509359 0.00009
NM_001953.5(TYMP):c.433G>A (p.Gly145Arg) rs121913037 0.00007
NM_000158.4(GBE1):c.1570C>T (p.Arg524Ter) rs137852888 0.00006
NM_000193.4(SHH):c.676G>A (p.Ala226Thr) rs104894043 0.00006
NM_000784.4(CYP27A1):c.410G>A (p.Arg137Gln) rs587778818 0.00004
NM_001953.5(TYMP):c.931G>A (p.Gly311Ser) rs121913040 0.00004
NM_004211.5(SLC6A5):c.1472A>G (p.Tyr491Cys) rs121908494 0.00004
NM_198578.4(LRRK2):c.6929C>T (p.Thr2310Met) rs200002022 0.00004
NM_000193.4(SHH):c.708C>A (p.Ser236Arg) rs587778806 0.00003
NM_000784.4(CYP27A1):c.380G>A (p.Arg127Gln) rs376230356 0.00003
NM_001127701.1(SERPINA1):c.194T>C (p.Leu65Pro) rs28931569 0.00003
NM_001953.5(TYMP):c.1160-1G>A rs797044455 0.00003
NM_033409.4(SLC52A3):c.1238T>C (p.Val413Ala) rs267606687 0.00003
NM_207352.4(CYP4V2):c.1523G>A (p.Arg508His) rs119103284 0.00003
NR_001566.3(TERC):n.37A>G rs199422261 0.00003
NM_000051.4(ATM):c.8786+1G>A rs17174393 0.00002
NM_000096.4(CP):c.229G>C (p.Asp77His) rs200683433 0.00002
NM_000158.4(GBE1):c.671T>C (p.Leu224Pro) rs137852886 0.00002
NM_000051.4(ATM):c.2T>C (p.Met1Thr) rs786203606 0.00001
NM_000096.4(CP):c.548T>C (p.Ile183Thr) rs386134123 0.00001
NM_000158.4(GBE1):c.1883A>G (p.His628Arg) rs137852891 0.00001
NM_000158.4(GBE1):c.771T>A (p.Phe257Leu) rs137852887 0.00001
NM_000193.4(SHH):c.1147G>A (p.Ala383Thr) rs137853341 0.00001
NM_000193.4(SHH):c.664G>A (p.Asp222Asn) rs587778805 0.00001
NM_000540.3(RYR1):c.13673G>A (p.Arg4558Gln) rs118192130 0.00001
NM_000540.3(RYR1):c.14818G>A (p.Ala4940Thr) rs118192158 0.00001
NM_000784.4(CYP27A1):c.1415G>C (p.Gly472Ala) rs200883871 0.00001
NM_000784.4(CYP27A1):c.1420C>T (p.Arg474Trp) rs121908098 0.00001
NM_000784.4(CYP27A1):c.409C>T (p.Arg137Trp) rs72551312 0.00001
NM_000784.4(CYP27A1):c.435G>T (p.Gly145=) rs587778796 0.00001
NM_000784.4(CYP27A1):c.745C>T (p.Gln249Ter) rs72551316 0.00001
NM_000784.4(CYP27A1):c.776A>G (p.Lys259Arg) rs72551317 0.00001
NM_001953.5(TYMP):c.1300+1G>A rs1064792878 0.00001
NM_001953.5(TYMP):c.228G>A (p.Met76Ile) rs1064792859 0.00001
NM_001953.5(TYMP):c.340G>A (p.Asp114Asn) rs1064792861 0.00001
NM_001953.5(TYMP):c.854T>C (p.Leu285Pro) rs121913042 0.00001
NM_001953.5(TYMP):c.865G>A (p.Glu289Lys) rs946234163 0.00001
NM_005506.4(SCARB2):c.1187+2dup rs727502783 0.00001
NM_033028.5(BBS4):c.42A>G (p.Val14=) rs113994181 0.00001
NM_054012.4(ASS1):c.970+5G>A rs372128852 0.00001
NM_207352.4(CYP4V2):c.1091-2A>G rs199476183 0.00001
NM_207352.4(CYP4V2):c.253C>T (p.Arg85Cys) rs199476186 0.00001
NM_207352.4(CYP4V2):c.283G>A (p.Gly95Arg) rs199476187 0.00001
NM_207352.4(CYP4V2):c.992A>C (p.His331Pro) rs199476197 0.00001
NR_001566.3(TERC):n.35C>T rs199422260 0.00001
NC_000003.12:g.169764651G>C rs199422286
NC_012920.1(MT-CYB):m.15257G>A rs41518645
NC_012920.1(MT-ND1):m.4216T>C rs1599988
NC_012920.1(MT-ND5):m.13708G>A rs28359178
NC_012920.1(MT-RNR1):m.961T>G rs3888511
NM_000051.4(ATM):c.2284_2285del (p.Leu762fs) rs587781658
NM_000051.4(ATM):c.6404_6405insTT (p.Leu2135_Arg2136insTer) rs587782554
NM_000096.4(CP):c.82A>T (p.Ile28Phe) rs386134121
NM_000096.4(CP):c.848G>C (p.Trp283Ser) rs386134126
NM_000155.4(GALT):c.-119_-116delGTCA rs111033640
NM_000158.4(GBE1):c.1634A>G (p.His545Arg) rs137852889
NM_000158.4(GBE1):c.691+5G>C rs397515344
NM_000193.4(SHH):c.562G>C (p.Glu188Gln) rs587778799
NM_000311.3(PRNP):c.204_227del24 (p.Pro84_Gln91del) rs193922906
NM_000500.9(CYP21A2):c.293-13C>G rs6467
NM_000500.9(CYP21A2):c.923dup (p.Leu308fs) rs267606756
NM_000530.8(MPZ):c.499G>C (p.Gly167Arg) rs121913586
NM_000532.5(PCCB):c.1218_1231delinsTAGAGCACAGGA (p.Gly407fs) rs397507445
NM_000540.3(RYR1):c.1209C>G (p.Ile403Met) rs118192116
NM_000540.3(RYR1):c.14387A>G (p.Tyr4796Cys) rs118192167
NM_000540.3(RYR1):c.14581C>T (p.Arg4861Cys) rs118192181
NM_000540.3(RYR1):c.14678G>A (p.Arg4893Gln) rs118192151
NM_000540.3(RYR1):c.14696G>A (p.Gly4899Glu) rs118192183
NM_000540.3(RYR1):c.14717C>T (p.Ala4906Val) rs118192153
NM_000540.3(RYR1):c.7522C>T (p.Arg2508Cys) rs118192178
NM_000602.4(SERPINE1):c.-820_-817G(4_5) rs1799762
NM_000784.4(CYP27A1):c.1183C>A (p.Arg395Ser) rs121908096
NM_000784.4(CYP27A1):c.1209C>G (p.Asn403Lys) rs587778781
NM_000784.4(CYP27A1):c.1435C>G (p.Arg479Gly) rs72551322
NM_000784.4(CYP27A1):c.373_379del (p.Pro125fs) rs587778794
NM_000784.4(CYP27A1):c.433G>A (p.Gly145Arg) rs587778795
NM_000784.4(CYP27A1):c.526del (p.Asp176fs) rs765512351
NM_000784.4(CYP27A1):c.944_948del (p.Leu315fs) rs397515356
NM_001032386.2(SUOX):c.1280_1281delinsAC (p.Ser427Tyr) rs1565799723
NM_001039958.2(MESP2):c.241G>T (p.Gly81Ter) rs118204034
NM_001048174.2(MUTYH):c.228C>A (p.Tyr76Ter) rs121908380
NM_001267550.2(TTN):c.95126C>G (p.Pro31709Arg) rs869320739
NM_001371596.2(MFSD8):c.881C>A (p.Thr294Lys) rs140948465
NM_001953.4(TYMP):c.929-6_929-3del rs201685922
NM_001953.5(TYMP):c.1160G>A (p.Gly387Asp) rs1064792873
NM_001953.5(TYMP):c.1187CGCTGG[1] (p.Ala398_Leu399del) rs786205098
NM_001953.5(TYMP):c.1301-1G>A rs773785934
NM_001953.5(TYMP):c.275C>A (p.Thr92Asn) rs891107196
NM_001953.5(TYMP):c.478T>C (p.Ser160Pro) rs1064792864
NM_001953.5(TYMP):c.518T>G (p.Met173Arg) rs1064792865
NM_001953.5(TYMP):c.893G>A (p.Gly298Asp) rs1064792872
NM_001953.5(TYMP):c.928+1G>A rs1064792876
NM_001953.5(TYMP):c.938T>C (p.Leu313Pro) rs892141220
NM_002739.5(PRKCG):c.188G>T (p.Gly63Val) rs386134159
NM_003977.4(AIP):c.804C>A (p.Tyr268Ter) rs121908356
NM_004409.4(DMPK):c.*224CTG[(35_49)]
NM_004937.3(CTNS):c.559_561+24del rs113994211
NM_005413.4(SIX3):c.770G>C (p.Arg257Pro) rs121917879
NM_006218.4(PIK3CA):c.1624G>A (p.Glu542Lys) rs121913273
NM_007272.3(CTRC):c.180C>A (p.Gly60=) rs497078
NM_012203.1(GRHPR):c.866-25CT[9] rs34302950
NM_015915.5(ATL1):c.1519dup (p.Ile507fs) rs863223314
NM_018965.4(TREM2):c.40+4_40+6del rs386834142
NM_020919.4(ALS2):c.470G>A (p.Cys157Tyr) rs121908138
NM_024649.5(BBS1):c.1340-2A>G rs113994180
NM_024649.5(BBS1):c.831-3C>G rs113994179
NM_033409.4(SLC52A3):c.568-16_568-15insCTGATTGAC rs3833341
NM_207352.4(CYP4V2):c.1526C>T (p.Pro509Leu) rs199476205
NR_001566.3(TERC):n.116C>T rs199422272
Single allele

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