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 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
103 21 26 41 11 0 23 68

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 7 4 0 0
likely pathogenic 3 1 6 0 0
likely benign 10 4 11 24 31

Submitter to submitter summary #

Total submitters: 29
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
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics 0 5 3 26 4 0 1 34
Illumina Clinical Services Laboratory,Illumina 0 2 16 8 2 0 1 27
PreventionGenetics 0 0 3 17 0 0 0 20
GeneDx 0 5 4 12 0 0 1 17
Laboratory for Molecular Medicine,Partners HealthCare Personalized Medicine 0 2 1 9 0 0 0 10
Soonchunhyang University Bucheon Hospital,Soonchunhyang University Medical Center 0 0 0 1 6 0 3 10
GeneReviews 0 0 1 4 0 0 3 8
Counsyl 0 2 2 1 1 0 3 7
OMIM 0 12 0 0 0 0 4 4
Genetic Services Laboratory, University of Chicago 0 0 3 0 1 0 0 4
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories 0 0 0 4 0 0 0 4
Invitae 0 0 1 3 0 0 0 4
PXE International 0 0 0 1 0 0 2 3
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics 0 0 0 2 1 0 0 3
Human Genetics - Radboudumc,Radboudumc 0 2 0 0 1 0 2 3
NIHR Bioresource Rare Diseases,University of Cambridge 0 0 1 1 0 0 1 3
Diagnostic Laboratory, Department of Genetics,University Medical Center Groningen 0 0 1 2 0 0 0 3
Ambry Genetics 0 0 0 2 0 0 0 2
Molecular Diagnostics Laboratory,Seoul National University Hospital 0 1 0 0 1 0 1 2
Genomic Research Center,Shahid Beheshti University of Medical Sciences 0 0 0 0 0 0 2 2
Institute of Human Genetics, Univ. Regensburg,Univ. Regensburg 0 0 0 2 0 0 0 2
CeGaT Praxis fuer Humangenetik Tuebingen 0 0 1 1 0 0 0 2
Baylor Miraca Genetics Laboratories, 0 0 1 0 0 0 0 1
Mayo Clinic Genetic Testing Laboratories,Mayo Clinic 0 0 0 1 0 0 0 1
UCLA Clinical Genomics Center, UCLA 0 0 0 0 0 0 1 1
Institute for Ophthalmic Research,University Tuebingen 0 0 0 0 0 0 1 1
Centre for Genomic Medicine, Manchester,Central Manchester University Hospitals 0 0 0 0 0 0 1 1
SIB Swiss Institute of Bioinformatics 0 0 0 1 0 0 0 1
Broad Institute Rare Disease Group,Broad Institute 0 0 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 68
Download table as spreadsheet
HGVS dbSNP
NM_000180.3(GUCY2D):c.154G>T (p.Ala52Ser) rs61749665
NM_000180.3(GUCY2D):c.164C>T (p.Thr55Met) rs201414567
NM_000180.3(GUCY2D):c.2101C>T (p.Pro701Ser) rs34598902
NM_000180.3(GUCY2D):c.61T>C (p.Trp21Arg) rs9905402
NM_000214.3(JAG1):c.1511A>G (p.Asn504Ser) rs527236046
NM_000214.3(JAG1):c.588C>T (p.Cys196=) rs1801138
NM_000214.3(JAG1):c.765C>T (p.Tyr255=) rs1131695
NM_000260.3(MYO7A):c.47T>C (p.Leu16Ser) rs1052030
NM_000260.3(MYO7A):c.4805G>A (p.Arg1602Gln) rs139889944
NM_000322.4(PRPH2):c.1013A>G (p.Asp338Gly) rs434102
NM_000322.4(PRPH2):c.499G>A (p.Gly167Ser) rs527236098
NM_000350.2(ABCA4):c.1268A>G (p.His423Arg) rs3112831
NM_000350.2(ABCA4):c.1294G>A (p.Glu432Lys) rs201117452
NM_000350.2(ABCA4):c.1699G>A (p.Val567Met) rs74516571
NM_000350.2(ABCA4):c.194G>A (p.Gly65Glu) rs62654395
NM_000350.2(ABCA4):c.3626T>C (p.Met1209Thr) rs76258939
NM_000350.2(ABCA4):c.4195G>A (p.Glu1399Lys) rs62642573
NM_000350.2(ABCA4):c.4283C>T (p.Thr1428Met) rs1800549
NM_000350.2(ABCA4):c.6119G>A (p.Arg2040Gln) rs148460146
NM_000350.2(ABCA4):c.6282+7G>A rs17110761
NM_000350.2(ABCA4):c.6445C>T (p.Arg2149Ter) rs61750654
NM_000350.2(ABCA4):c.6764G>T (p.Ser2255Ile) rs6666652
NM_000539.3(RHO):c.891C>T (p.Ser297=) rs142285818
NM_000541.4(SAG):c.250C>T (p.Arg84Cys) rs115857633
NM_000554.4(CRX):c.365G>A (p.Gly122Asp) rs61748441
NM_000843.4(GRM6):c.1227C>T (p.Tyr409=) rs2645339
NM_001034853.1(RPGR):c.223A>G (p.Ile75Val) rs111631988
NM_001034853.1(RPGR):c.785C>G (p.Ala262Gly) rs138018739
NM_001077182.2(FSCN2):c.72delG (p.Thr25Glnfs) rs376633374
NM_001077620.2(PRCD):c.2T>C (p.Met1Thr) rs527236092
NM_001142564.1(CNGA1):c.398delG (p.Gly133Valfs) rs527236058
NM_001142800.1(EYS):c.3489T>A (p.Asn1163Lys) rs150951106
NM_001171.5(ABCC6):c.3803G>A (p.Arg1268Gln) rs2238472
NM_001171.5(ABCC6):c.4069C>T (p.Arg1357Trp) rs63750428
NM_001171.5(ABCC6):c.793A>G (p.Arg265Gly) rs72657698
NM_002098.5(GUCA1B):c.469G>A (p.Gly157Arg) rs121909124
NM_006005.3(WFS1):c.2209G>A (p.Glu737Lys) rs147834269
NM_006269.1(RP1):c.5008G>A (p.Ala1670Thr) rs446227
NM_006343.2(MERTK):c.1450G>A (p.Gly484Ser) rs527236084
NM_012193.3(FZD4):c.205C>T (p.His69Tyr) rs80358282
NM_014014.4(SNRNP200):c.1871G>A (p.Arg624Lys) rs527236115
NM_014249.3(NR2E3):c.361G>A (p.Glu121Lys) rs146403122
NM_014249.3(NR2E3):c.364C>T (p.Arg122Cys) rs527236086
NM_015272.4(RPGRIP1L):c.3790G>A (p.Asp1264Asn) rs3213758
NM_016247.3(IMPG2):c.3262C>T (p.Arg1088Ter) rs199867882
NM_017651.4(AHI1):c.3257A>G (p.Glu1086Gly) rs148000791
NM_019098.4(CNGB3):c.1208G>A rs147876778
NM_022124.5(CDH23):c.5418C>G (p.Asp1806Glu) rs74145660
NM_025114.3(CEP290):c.6787A>G (p.Ser2263Gly) rs77778467
NM_025114.3(CEP290):c.829G>C (p.Glu277Gln) rs45502896
NM_025136.3(OPA3):c.231T>C (p.Ala77=) rs3826860
NM_031433.3(MFRP):c.492C>T (p.Tyr164=) rs36015759
NM_032119.3(ADGRV1):c.7006C>T (p.Arg2336Ter) rs527236133
NM_033028.4(BBS4):c.1061T>C (p.Ile354Thr) rs2277598
NM_033028.4(BBS4):c.1414A>G (p.Met472Val) rs2277596
NM_133497.3(KCNV2):c.80G>A (p.Arg27His) rs145731729
NM_170784.2(MKKS):c.117C>T (p.Pro39=) rs16991547
NM_170784.2(MKKS):c.534C>T (p.Ile178=) rs17852625
NM_178857.5(RP1L1):c.4273G>C (p.Asp1425His) rs201205913
NM_206933.2(USH2A):c.11156G>A (p.Arg3719His) rs527236139
NM_206933.2(USH2A):c.13010C>T (p.Thr4337Met) rs527236137
NM_206933.2(USH2A):c.14243C>T (p.Ser4748Phe) rs527236126
NM_206933.2(USH2A):c.15233C>G (p.Pro5078Arg) rs527236122
NM_206933.2(USH2A):c.2802T>G (p.Cys934Trp) rs201527662
NM_206933.2(USH2A):c.688G>A (p.Val230Met) rs45500891
NM_207352.3(CYP4V2):c.367A>G (p.Met123Val) rs149684063
NM_207352.3(CYP4V2):c.64C>G (p.Leu22Val) rs1055138
NM_207352.3(CYP4V2):c.802-8_810del17insGC rs207482233

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