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:
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
110 11 32 52 12 0 10 71

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 likely benign benign
pathogenic 1 4 3 0 0
likely pathogenic 3 3 2 0 2
likely benign 4 1 12 28 45

Submitter to submitter summary #

Total submitters: 34
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 3 1 30 3 0 2 36
Invitae 0 1 4 25 2 0 3 34
Eurofins Ntd Llc (ga) 0 0 3 26 4 0 0 33
PreventionGenetics, part of Exact Sciences 0 1 7 20 0 0 0 27
Illumina Laboratory Services, Illumina 0 2 5 4 2 0 4 15
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ 0 1 1 11 0 0 0 12
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 0 1 6 3 2 0 0 11
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories 0 0 0 10 0 0 0 10
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center 0 0 1 9 0 0 0 10
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine 0 1 1 7 1 0 0 9
Clinical Genetics, Academic Medical Center 0 0 1 8 0 0 0 9
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen 0 0 0 9 0 0 0 9
CeGaT Center for Human Genetics Tuebingen 0 0 1 5 2 0 0 8
Genome Diagnostics Laboratory, University Medical Center Utrecht 0 0 2 5 0 0 0 7
Genetic Services Laboratory, University of Chicago 0 0 4 0 0 0 0 4
Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet 0 2 2 1 0 0 0 3
Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics 0 0 0 2 1 0 0 3
Athena Diagnostics Inc 0 0 0 2 0 0 0 2
Ambry Genetics 0 0 0 2 0 0 0 2
Mendelics 0 0 0 2 0 0 0 2
Institute of Human Genetics, Univ. Regensburg, Univ. Regensburg 0 0 0 2 0 0 0 2
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) 0 0 2 0 0 0 0 2
MGZ Medical Genetics Center 0 0 0 1 0 0 0 1
Natera, Inc. 0 3 0 1 0 0 0 1
GeneReviews 0 0 1 0 0 0 0 1
Mayo Clinic Laboratories, Mayo Clinic 0 0 0 1 0 0 0 1
Soonchunhyang University Bucheon Hospital, Soonchunhyang University Medical Center 0 0 0 0 0 0 1 1
Centre for Mendelian Genomics, University Medical Centre Ljubljana 0 0 0 0 0 0 1 1
NIHR Bioresource Rare Diseases, University of Cambridge 0 0 0 0 0 0 1 1
Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard 0 0 0 1 0 0 0 1
Genome-Nilou Lab 0 2 1 0 0 0 0 1
Faculty of Health Sciences, Beirut Arab University 0 0 0 0 0 0 1 1
3billion 0 2 1 0 0 0 0 1
Neuberg Supratech Reference Laboratories Pvt Ltd, Neuberg Centre for Genomic Medicine 0 0 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 71
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_000322.5(PRPH2):c.1013A>G (p.Asp338Gly) rs434102 0.77412
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 0.46276
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 0.25928
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 0.21425
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 0.14082
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 0.00614
NM_000541.5(SAG):c.250C>T (p.Arg84Cys) rs115857633 0.00530
NM_014249.4(NR2E3):c.361G>A (p.Glu121Lys) rs146403122 0.00472
NM_000350.3(ABCA4):c.3626T>C (p.Met1209Thr) rs76258939 0.00185
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_000180.4(GUCY2D):c.164C>T (p.Thr55Met) rs201414567 0.00047
NM_133497.4(KCNV2):c.80G>A (p.Arg27His) rs145731729 0.00044
NM_000539.3(RHO):c.891C>T (p.Ser297=) rs142285818 0.00041
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_000350.3(ABCA4):c.6119G>A (p.Arg2040Gln) rs148460146 0.00024
NM_012418.4(FSCN2):c.72del (p.Thr25fs) rs376633374 0.00024
NM_025114.4(CEP290):c.6787A>G (p.Ser2263Gly) rs77778467 0.00022
NM_207352.4(CYP4V2):c.367A>G (p.Met123Val) rs149684063 0.00021
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_004727.3(SLC24A1):c.2326G>C (p.Glu776Gln) rs150992293 0.00012
NM_006269.2(RP1):c.5797C>T (p.Arg1933Ter) rs118031911 0.00008
NM_206933.4(USH2A):c.11156G>A (p.Arg3719His) rs527236139 0.00006
NM_206933.4(USH2A):c.2802T>G (p.Cys934Trp) rs201527662 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_000214.3(JAG1):c.1511A>G (p.Asn504Ser) rs527236046 0.00004
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_001379270.1(CNGA1):c.827G>A (p.Arg276His) rs375412499 0.00004
NM_002098.6(GUCA1B):c.469G>A (p.Gly157Arg) rs121909124 0.00004
NM_000350.3(ABCA4):c.4195G>A (p.Glu1399Lys) rs62642573 0.00003
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_006343.3(MERTK):c.1450G>A (p.Gly484Ser) rs527236084 0.00001
NM_000283.4(PDE6B):c.1576G>A (p.Glu526Lys) rs527236091
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_018418.4(SPATA7):c.20_23del rs527236050
NM_022124.6(CDH23):c.5418C>G (p.Asp1806Glu) rs74145660
NM_032119.4(ADGRV1):c.7006C>T (p.Arg2336Ter) rs527236133
NM_207352.4(CYP4V2):c.802-8_810delinsGC rs207482233

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