ClinVar Miner

Variants from Department of Ophthalmology and Visual Sciences Kyoto University with conflicting interpretations

Location: Japan  Primary collection method: not provided
Minimum review status of the submission from Department of Ophthalmology and Visual Sciences Kyoto University: Collection method of the submission from Department of Ophthalmology and Visual Sciences Kyoto University:
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
109 16 0 53 12 0 10 67

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
Department of Ophthalmology and Visual Sciences Kyoto University pathogenic likely pathogenic uncertain significance benign
pathogenic 0 5 3 0
likely pathogenic 3 0 2 1
likely benign 5 2 12 45

Submitter to submitter summary #

Total submitters: 38
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 4 0 30 4 0 2 36
Eurofins Ntd Llc (ga) 0 3 0 26 4 0 0 30
Labcorp Genetics (formerly Invitae), Labcorp 0 5 0 25 2 0 3 30
PreventionGenetics, part of Exact Sciences 0 8 0 20 0 0 1 21
Breakthrough Genomics, Breakthrough Genomics 0 16 0 16 1 0 0 17
Mayo Clinic Laboratories, Mayo Clinic 0 1 0 13 0 0 0 13
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ 0 2 0 11 0 0 0 11
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories 0 0 0 10 0 0 0 10
CeGaT Center for Human Genetics Tuebingen 0 3 0 7 2 0 0 9
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center 0 1 0 9 0 0 0 9
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen 0 0 0 9 0 0 0 9
Clinical Genetics, Academic Medical Center 0 1 0 8 0 0 0 8
Illumina Laboratory Services, Illumina 0 7 0 4 2 0 2 8
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine 0 2 0 7 1 0 0 8
Genome Diagnostics Laboratory, University Medical Center Utrecht 0 2 0 5 0 0 0 5
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 0 14 0 3 2 0 0 5
Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics 0 0 0 2 1 0 0 3
Ambry Genetics 0 0 0 2 0 0 0 2
Athena Diagnostics 0 0 0 2 0 0 0 2
Dasa 0 1 0 0 0 0 2 2
Institute of Human Genetics, Univ. Regensburg, Univ. Regensburg 0 0 0 2 0 0 0 2
Mendelics 0 0 0 2 0 0 0 2
Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard 0 0 0 1 0 0 0 1
Centre for Mendelian Genomics, University Medical Centre Ljubljana 0 0 0 0 0 0 1 1
Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet 0 4 0 1 0 0 0 1
Department of Reproductive Genetics, International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine 0 0 0 1 0 0 0 1
Faculty of Health Sciences, Beirut Arab University 0 0 0 0 0 0 1 1
Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre 0 0 0 1 0 0 0 1
Genomic Research Center, Shahid Beheshti University of Medical Sciences 0 0 0 0 0 0 1 1
Laboratory of Genetics, Children's Clinical University Hospital Latvia 0 0 0 1 0 0 0 1
Laboratory of Medical Genetics, National & Kapodistrian University of Athens 0 0 0 1 0 0 0 1
MGZ Medical Genetics Center 0 0 0 1 0 0 0 1
NIHR Bioresource Rare Diseases, University of Cambridge 0 0 0 0 0 0 1 1
Natera, Inc. 0 2 0 1 0 0 0 1
Neuberg Centre For Genomic Medicine, NCGM 0 0 0 1 0 0 0 1
SingHealth Duke-NUS Institute of Precision Medicine 0 3 0 1 0 0 0 1
Soonchunhyang University Bucheon Hospital, Soonchunhyang University Medical Center 0 0 0 0 0 0 1 1
Variantyx, Inc. 0 0 0 0 0 0 1 1

All variants with conflicting interpretations #

Total variants: 67
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_000322.5(PRPH2):c.1013A>G (p.Asp338Gly) rs434102 0.77333
NM_025136.4(OPA3):c.231T>C (p.Ala77=) rs3826860 0.70508
NM_033028.5(BBS4):c.1061T>C (p.Ile354Thr) rs2277598 0.52665
NM_000843.4(GRM6):c.1227C>T (p.Tyr409=) rs2645339 0.49941
NM_000260.4(MYO7A):c.47T>C (p.Leu16Ser) rs1052030 0.47208
NM_207352.4(CYP4V2):c.64C>G (p.Leu22Val) rs1055138 0.45965
NM_000214.3(JAG1):c.765C>T (p.Tyr255=) rs1131695 0.42930
NM_001171.6(ABCC6):c.1233T>C (p.Asn411=) rs9930886 0.31672
NM_000180.4(GUCY2D):c.154G>T (p.Ala52Ser) rs61749665 0.29501
NM_000350.3(ABCA4):c.1268A>G (p.His423Arg) rs3112831 0.25794
NM_031433.4(MFRP):c.492C>T (p.Tyr164=) rs36015759 0.23503
NM_001171.6(ABCC6):c.3803G>A (p.Arg1268Gln) rs2238472 0.22903
NM_006269.2(RP1):c.5008G>A (p.Ala1670Thr) rs446227 0.21985
NM_170784.3(MKKS):c.117C>T (p.Pro39=) rs16991547 0.18435
NM_000350.3(ABCA4):c.6764G>T (p.Ser2255Ile) rs6666652 0.17582
NM_170784.3(MKKS):c.534C>T (p.Ile178=) rs17852625 0.14499
NM_000350.3(ABCA4):c.6282+7G>A rs17110761 0.13306
NM_001034853.2(RPGR):c.3396C>T (p.Asn1132=) rs12687163 0.12023
NM_000214.3(JAG1):c.588C>T (p.Cys196=) rs1801138 0.10620
NM_000180.4(GUCY2D):c.61T>C (p.Trp21Arg) rs9905402 0.09880
NM_001171.6(ABCC6):c.793A>G (p.Arg265Gly) rs72657698 0.06836
NM_015272.5(RPGRIP1L):c.3790G>A (p.Asp1264Asn) rs3213758 0.04663
NM_000180.4(GUCY2D):c.2101C>T (p.Pro701Ser) rs34598902 0.03505
NM_001034853.2(RPGR):c.223A>G (p.Ile75Val) rs111631988 0.03363
NM_025114.4(CEP290):c.829G>C (p.Glu277Gln) rs45502896 0.01608
NM_206933.4(USH2A):c.688G>A (p.Val230Met) rs45500891 0.01191
NM_000554.6(CRX):c.365G>A (p.Gly122Asp) rs61748441 0.00617
NM_000541.5(SAG):c.250C>T (p.Arg84Cys) rs115857633 0.00502
NM_014249.4(NR2E3):c.361G>A (p.Glu121Lys) rs146403122 0.00472
NM_000350.3(ABCA4):c.3626T>C (p.Met1209Thr) rs76258939 0.00222
NM_000350.3(ABCA4):c.4283C>T (p.Thr1428Met) rs1800549 0.00160
NM_000260.4(MYO7A):c.4805G>A (p.Arg1602Gln) rs139889944 0.00121
NM_019098.5(CNGB3):c.1208G>A (p.Arg403Gln) rs147876778 0.00119
NM_001134831.2(AHI1):c.3257A>G (p.Glu1086Gly) rs148000791 0.00115
NM_001142800.2(EYS):c.3489T>A (p.Asn1163Lys) rs150951106 0.00076
NM_133497.4(KCNV2):c.80G>A (p.Arg27His) rs145731729 0.00061
NM_000180.4(GUCY2D):c.164C>T (p.Thr55Met) rs201414567 0.00057
NM_000539.3(RHO):c.891C>T (p.Ser297=) rs142285818 0.00041
NM_012418.4(FSCN2):c.72del (p.Thr25fs) rs376633374 0.00040
NM_001034853.2(RPGR):c.785C>G (p.Ala262Gly) rs138018739 0.00035
NM_033028.5(BBS4):c.1414A>G (p.Met472Val) rs2277596 0.00034
NM_000327.4(ROM1):c.339dup (p.Leu114fs) rs71458427 0.00033
NM_207352.4(CYP4V2):c.367A>G (p.Met123Val) rs149684063 0.00027
NM_000350.3(ABCA4):c.6119G>A (p.Arg2040Gln) rs148460146 0.00024
NM_025114.4(CEP290):c.6787A>G (p.Ser2263Gly) rs77778467 0.00022
NM_006005.3(WFS1):c.2209G>A (p.Glu737Lys) rs147834269 0.00018
NM_012193.4(FZD4):c.205C>T (p.His69Tyr) rs80358282 0.00014
NM_001142800.2(EYS):c.9209T>C (p.Ile3070Thr) rs183589498 0.00013
NM_206933.4(USH2A):c.2802T>G (p.Cys934Trp) rs201527662 0.00013
NM_002098.6(GUCA1B):c.469G>A (p.Gly157Arg) rs121909124 0.00008
NM_206933.4(USH2A):c.11156G>A (p.Arg3719His) rs527236139 0.00006
NM_000350.3(ABCA4):c.1294G>A (p.Glu432Lys) rs201117452 0.00005
NM_006269.2(RP1):c.1186C>T (p.Arg396Ter) rs201493928 0.00005
NM_000350.3(ABCA4):c.1699G>A (p.Val567Met) rs74516571 0.00004
NM_001171.6(ABCC6):c.4069C>T (p.Arg1357Trp) rs63750428 0.00004
NM_000350.3(ABCA4):c.4195G>A (p.Glu1399Lys) rs62642573 0.00003
NM_001379270.1(CNGA1):c.827G>A (p.Arg276His) rs375412499 0.00003
NM_000214.3(JAG1):c.1511A>G (p.Asn504Ser) rs527236046 0.00001
NM_000350.3(ABCA4):c.6445C>T (p.Arg2149Ter) rs61750654 0.00001
NM_001171.6(ABCC6):c.1760C>G (p.Ser587Cys) rs527236047 0.00001
NM_006005.3(WFS1):c.1234G>C (p.Val412Leu) rs149865710 0.00001
NM_000350.3(ABCA4):c.194G>A (p.Gly65Glu) rs62654395
NM_001142800.2(EYS):c.4957dup (p.Ser1653fs) rs527236065
NM_005802.5(TOPORS):c.2554_2557del (p.Glu852fs) rs527236116
NM_018418.5(SPATA7):c.20_23delTCAG rs527236050
NM_022124.6(CDH23):c.5418C>G (p.Asp1806Glu) rs74145660
NM_032119.4(ADGRV1):c.7006C>T (p.Arg2336Ter) rs527236133

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