ClinVar Miner

Variants from Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet with conflicting interpretations

Location: Denmark  Primary collection method: research
Minimum review status of the submission from Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet: Collection method of the submission from Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet:
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
545 72 2 75 6 2 39 117

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 Clinical Genetics, Copenhagen University Hospital, Rigshospitalet pathogenic likely pathogenic uncertain significance likely benign benign affects pathogenic, low penetrance risk factor
pathogenic 0 26 3 1 0 0 0 0
likely pathogenic 49 2 15 2 3 0 1 1
uncertain significance 8 12 0 6 3 1 0 0
benign 0 0 0 1 0 0 0 0

Submitter to submitter summary #

Total submitters: 64
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
Invitae 0 26 0 12 3 1 6 22
NIHR Bioresource Rare Diseases, University of Cambridge 0 22 0 11 0 0 5 16
GeneDx 0 12 0 6 3 0 5 14
OMIM 0 6 0 10 0 2 1 13
Illumina Laboratory Services, Illumina 0 20 0 4 1 0 6 11
CeGaT Center for Human Genetics Tuebingen 0 12 0 5 3 0 2 10
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ 0 11 0 6 2 0 2 10
Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard 0 14 0 7 0 0 3 10
Institute of Human Genetics, University of Leipzig Medical Center 0 2 0 7 0 0 2 9
Sharon lab, Hadassah-Hebrew University Medical Center 0 15 0 8 0 0 1 9
PreventionGenetics, part of Exact Sciences 0 5 0 4 2 0 2 8
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 0 13 0 2 1 0 5 8
Mendelics 0 4 0 6 0 0 2 8
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories 0 1 0 5 2 0 0 7
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center 0 8 0 2 3 0 2 7
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine 0 8 0 4 2 0 0 6
Clinical Genetics, Academic Medical Center 0 8 0 2 3 0 1 6
Eurofins Ntd Llc (ga) 0 10 0 2 2 0 2 6
Leiden Open Variation Database 0 3 0 5 0 0 1 6
Institute of Medical Molecular Genetics, University of Zurich 0 5 0 5 0 0 0 5
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen 0 10 0 4 0 0 1 5
Blueprint Genetics 0 6 0 2 0 0 2 4
Institute of Human Genetics, Univ. Regensburg, Univ. Regensburg 0 10 0 4 0 0 0 4
3billion 0 4 0 4 0 0 0 4
Revvity Omics, Revvity 0 4 0 2 0 0 1 3
Department of Ophthalmology and Visual Sciences Kyoto University 0 2 2 1 0 0 0 3
Genetics and Molecular Pathology, SA Pathology 0 1 0 3 0 0 0 3
Ocular Genomics Institute, Massachusetts Eye and Ear 0 2 0 3 0 0 0 3
Houlden Lab, UCL Institute of Neurology 0 0 0 1 0 0 2 3
Baylor Genetics 0 1 0 0 0 0 2 2
Athena Diagnostics Inc 0 2 0 0 2 0 0 2
Molecular Genetics Laboratory, Institute for Ophthalmic Research 0 1 0 2 0 0 0 2
MGZ Medical Genetics Center 0 5 0 2 0 0 0 2
Natera, Inc. 0 8 0 2 0 0 0 2
Department of Pathology and Laboratory Medicine, Sinai Health System 0 0 0 1 0 0 1 2
Ophthalmic Genetics Group, Institute of Molecular and Clinical Ophthalmology Basel 0 11 0 2 0 0 0 2
Dept Of Ophthalmology, Nagoya University 0 0 0 2 0 0 0 2
Genetic Services Laboratory, University of Chicago 0 1 0 0 0 0 1 1
Centogene AG - the Rare Disease Company 0 0 0 0 0 0 1 1
Counsyl 0 0 0 1 0 0 0 1
Sema4, Sema4 0 0 0 1 0 0 0 1
NEI Ophthalmic Genomics Laboratory, National Institutes of Health 0 1 0 0 0 0 1 1
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute 0 4 0 1 0 0 0 1
Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München 0 0 0 1 0 0 0 1
Lupski Lab, Baylor-Hopkins CMG, Baylor College of Medicine 0 0 0 1 0 0 0 1
Centre for Genomic Medicine, Manchester, Central Manchester University Hospitals 0 0 0 1 0 0 0 1
Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics 0 1 0 0 0 0 1 1
Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin 0 0 0 1 0 0 0 1
Rui Chen Lab, Baylor College of Medicine 0 0 0 1 0 0 0 1
Color Diagnostics, LLC DBA Color Health 0 0 0 1 0 0 0 1
Laboratoire de Génétique Moléculaire, CHU Bordeaux 0 0 0 1 0 0 0 1
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen 0 1 0 1 0 0 0 1
Medical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia 0 2 0 1 0 0 0 1
Variantyx, Inc. 0 0 0 1 0 0 0 1
Department Of Genetics, Sultan Qaboos University Hospital, Sultan Qaboos University 0 0 0 1 0 0 0 1
Laboratory of Medical Genetics, National & Kapodistrian University of Athens 0 1 0 1 0 0 0 1
Al Jalila Children's Genomics Center, Al Jalila Childrens Speciality Hospital 0 0 0 0 0 0 1 1
Institute of Human Genetics, University Hospital Muenster 0 2 0 1 0 0 0 1
Laboratory of Genetics in Ophthalmology, Institut Imagine 0 0 0 1 0 0 0 1
New York Genome Center 0 0 0 0 0 0 1 1
MNM Diagnostics 0 0 0 0 0 0 1 1
Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center 0 0 0 1 0 0 0 1
Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein 0 1 0 0 0 0 1 1
Arcensus 0 0 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 117
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_206933.4(USH2A):c.2522C>A (p.Ser841Tyr) rs111033282 0.00569
NM_033100.4(CDHR1):c.783G>A (p.Pro261=) rs147346345 0.00446
NM_000350.3(ABCA4):c.2588G>C (p.Gly863Ala) rs76157638 0.00445
NM_001142800.2(EYS):c.977G>A (p.Ser326Asn) rs112822256 0.00379
NM_206933.4(USH2A):c.15433G>A (p.Val5145Ile) rs111033269 0.00379
NM_206933.4(USH2A):c.5975A>G (p.Tyr1992Cys) rs41303287 0.00356
NM_172364.5(CACNA2D4):c.2120G>A (p.Arg707His) rs76064926 0.00329
NM_000440.3(PDE6A):c.878C>T (p.Pro293Leu) rs114973968 0.00309
NM_000350.3(ABCA4):c.5882G>A (p.Gly1961Glu) rs1800553 0.00269
NM_000180.4(GUCY2D):c.74C>T (p.Ser25Phe) rs557108466 0.00228
NM_024649.5(BBS1):c.1169T>G (p.Met390Arg) rs113624356 0.00212
NM_000350.3(ABCA4):c.3113C>T (p.Ala1038Val) rs61751374 0.00178
NM_000350.3(ABCA4):c.5693G>A (p.Arg1898His) rs1800552 0.00153
NM_206933.4(USH2A):c.2276G>T (p.Cys759Phe) rs80338902 0.00137
NM_000350.3(ABCA4):c.4685T>C (p.Ile1562Thr) rs1762111 0.00132
NM_001384910.1(GUCA1A):c.149C>T (p.Pro50Leu) rs104893968 0.00130
NM_001297.5(CNGB1):c.2957A>T (p.Asn986Ile) rs201162411 0.00116
NM_000883.4(IMPDH1):c.1598A>G (p.Gln533Arg) rs144498273 0.00088
NM_017777.4(MKS1):c.857A>G (p.Asp286Gly) rs151023718 0.00083
NM_001297.5(CNGB1):c.2747G>A (p.Arg916His) rs137853902 0.00071
NM_144596.4(TTC8):c.1327C>T (p.Arg443Trp) rs140698625 0.00064
NM_201253.3(CRB1):c.614T>C (p.Ile205Thr) rs62645749 0.00049
NM_000350.3(ABCA4):c.6089G>A (p.Arg2030Gln) rs61750641 0.00048
NM_206933.4(USH2A):c.12575G>A (p.Arg4192His) rs199605265 0.00046
NM_025150.5(TARS2):c.773C>T (p.Ser258Leu) rs145039072 0.00042
NM_201548.5(CERKL):c.769C>T (p.Arg257Ter) rs121909398 0.00039
NM_000350.3(ABCA4):c.5714+5G>A rs61751407 0.00036
NM_201253.3(CRB1):c.135C>G (p.Cys45Trp) rs145141811 0.00035
NM_001142800.2(EYS):c.2137+1G>A rs199740930 0.00034
NM_000350.3(ABCA4):c.5461-10T>C rs1800728 0.00031
NM_025150.5(TARS2):c.1354C>T (p.Arg452Trp) rs146503501 0.00028
NM_000059.4(BRCA2):c.5070A>C (p.Lys1690Asn) rs56087561 0.00023
NM_000350.3(ABCA4):c.4139C>T (p.Pro1380Leu) rs61750130 0.00023
NM_000180.4(GUCY2D):c.2302C>T (p.Arg768Trp) rs61750168 0.00019
NM_001256789.3(CACNA1F):c.3236+3G>A rs199932603 0.00019
NM_000350.3(ABCA4):c.1622T>C (p.Leu541Pro) rs61751392 0.00017
NM_000350.3(ABCA4):c.5196+1137G>A rs778234759 0.00013
NM_003322.6(TULP1):c.1496-6C>A rs281865171 0.00011
NM_000322.5(PRPH2):c.623G>A (p.Gly208Asp) rs139185976 0.00010
NM_000350.3(ABCA4):c.634C>T (p.Arg212Cys) rs61750200 0.00008
NM_000350.3(ABCA4):c.2453G>A (p.Gly818Glu) rs61750202 0.00006
NM_000350.3(ABCA4):c.768G>T (p.Val256=) rs62645944 0.00006
NM_206933.4(USH2A):c.10561T>C (p.Trp3521Arg) rs111033264 0.00006
NM_206933.4(USH2A):c.14219C>A (p.Ala4740Asp) rs539192853 0.00006
NM_000350.3(ABCA4):c.4773+3A>G rs759672616 0.00004
NM_001142800.2(EYS):c.7949C>T (p.Ser2650Phe) rs374714909 0.00004
NM_025150.5(TARS2):c.1285C>T (p.Arg429Ter) rs1382181446 0.00004
NM_201253.3(CRB1):c.2290C>T (p.Arg764Cys) rs62635654 0.00004
NM_206933.4(USH2A):c.7595-2144A>G rs786200928 0.00004
NM_000350.3(ABCA4):c.4918C>T (p.Arg1640Trp) rs61751404 0.00003
NM_001142800.2(EYS):c.6714del (p.Ile2239fs) rs752953889 0.00003
NM_001142800.2(EYS):c.2528G>A (p.Gly843Glu) rs74419361 0.00002
NM_001142800.2(EYS):c.9344T>A (p.Val3115Asp) rs748838955 0.00002
NM_004183.4(BEST1):c.140G>A (p.Arg47His) rs28940278 0.00002
NM_016247.4(IMPG2):c.2890C>T (p.Arg964Ter) rs267606875 0.00002
NM_016247.4(IMPG2):c.911G>A (p.Gly304Asp) rs749723076 0.00002
NM_025150.5(TARS2):c.968T>G (p.Phe323Cys) rs760208518 0.00002
NM_198428.3(BBS9):c.223C>T (p.Arg75Ter) rs775081992 0.00002
NM_000322.5(PRPH2):c.424C>T (p.Arg142Trp) rs61755783 0.00001
NM_000350.3(ABCA4):c.4919G>A (p.Arg1640Gln) rs61751403 0.00001
NM_000350.3(ABCA4):c.5316G>A (p.Trp1772Ter) rs61750571 0.00001
NM_000350.3(ABCA4):c.6088C>T (p.Arg2030Ter) rs61751383 0.00001
NM_000350.3(ABCA4):c.6118C>T (p.Arg2040Ter) rs61753038 0.00001
NM_001242957.3(MAK):c.814C>T (p.Arg272Ter) rs753314164 0.00001
NM_001297.5(CNGB1):c.2285G>A (p.Arg762His) rs760373259 0.00001
NM_005529.7(HSPG2):c.9109C>T (p.Gln3037Ter) rs898553156 0.00001
NM_006269.2(RP1):c.788-2A>T rs1422250479 0.00001
NM_006343.3(MERTK):c.1450G>A (p.Gly484Ser) rs527236084 0.00001
NM_025074.7(FRAS1):c.7551T>A (p.Tyr2517Ter) rs745597204 0.00001
NM_025150.5(TARS2):c.1838C>T (p.Pro613Leu) rs767519084 0.00001
NM_025150.5(TARS2):c.695+3A>G rs587777594 0.00001
NC_000018.9:g.77748581_77748614del34 rs535089924
NM_000051.4(ATM):c.478_482del (p.Ser160fs) rs587780624
NM_000180.4(GUCY2D):c.2513G>A (p.Arg838His) rs61750173
NM_000283.4(PDE6B):c.1576G>A (p.Glu526Lys) rs527236091
NM_000283.4(PDE6B):c.1923_1969delinsTCTGGG (p.Asn643fs) rs869312177
NM_000322.5(PRPH2):c.276dup (p.Arg93fs) rs1582780842
NM_000322.5(PRPH2):c.515G>A (p.Arg172Gln) rs61755793
NM_000322.5(PRPH2):c.646C>T (p.Pro216Ser) rs61755805
NM_000322.5(PRPH2):c.658C>T (p.Arg220Trp) rs61755809
NM_000322.5(PRPH2):c.715C>T (p.Gln239Ter) rs61755814
NM_000322.5(PRPH2):c.808_818del (p.Leu270fs) rs1582764504
NM_000322.5(PRPH2):c.811del (p.Leu271fs) rs1582764528
NM_000322.5(PRPH2):c.995T>A (p.Val332Glu) rs1582759492
NM_000350.3(ABCA4):c.5584+6T>C rs61750633
NM_000350.3(ABCA4):c.6386+1G>A rs745654673
NM_000539.3(RHO):c.541G>A (p.Glu181Lys) rs775557680
NM_000548.5(TSC2):c.1257+5G>A rs2151157428
NM_001083962.2(TCF4):c.655+1G>A rs587784465
NM_001101.5(ACTB):c.826G>A (p.Glu276Lys) rs1554329216
NM_001142800.2(EYS):c.1211dup (p.Asn404fs) rs764163418
NM_001142800.2(EYS):c.2000G>A (p.Arg667His) rs549456693
NM_001142800.2(EYS):c.4350_4356del (p.Ile1451fs) rs761238771
NM_001142800.2(EYS):c.4957dup (p.Ser1653fs) rs527236065
NM_001194998.2(CEP152):c.467dup (p.Gln157fs) rs1208144689
NM_001197104.2(KMT2A):c.4171C>T (p.Gln1391Ter) rs2134311608
NM_001330260.2(SCN8A):c.5620G>C (p.Val1874Leu) rs781602116
NM_001379270.1(CNGA1):c.947C>T (p.Ser316Phe) rs62625014
NM_002968.3(SALL1):c.601C>T (p.Gln201Ter) rs2143450145
NM_004183.4(BEST1):c.253T>C (p.Tyr85His) rs28940274
NM_004183.4(BEST1):c.287A>G (p.Gln96Arg) rs1225032182
NM_004183.4(BEST1):c.728C>T (p.Ala243Val) rs28940570
NM_004183.4(BEST1):c.887A>G (p.Asn296Ser) rs281865255
NM_004656.4(BAP1):c.422A>G (p.His141Arg) rs1705201896
NM_005802.5(TOPORS):c.2554_2557del (p.Glu852fs) rs527236116
NM_006245.4(PPP2R5D):c.751G>T (p.Asp251Tyr) rs1762178916
NM_012318.3(LETM1):c.2220G>C (p.Ter740Tyr) rs2108832865
NM_013275.6(ANKRD11):c.3787_3788del (p.Glu1263fs) rs2151753260
NM_014014.5(SNRNP200):c.2041C>T (p.Arg681Cys) rs959069360
NM_016247.4(IMPG2):c.534-13dup rs567795716
NM_024649.5(BBS1):c.1110+3G>C rs762276925
NM_025114.4(CEP290):c.180+1G>A rs758593134
NM_025150.5(TARS2):c.1274A>G (p.Glu425Gly) rs2102494691
NM_032271.3(TRAF7):c.1798G>A (p.Gly600Ser) rs2141298527
NM_033100.4(CDHR1):c.2522_2528del (p.Ile841fs) rs794727197
NM_201253.3(CRB1):c.613_619del (p.Ile205fs) rs62645752
UGT1A1*28 rs3064744

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