ClinVar Miner

Variants from Department of Genetics, Rouen University Hospital, Normandy Center for Genomic and Personalized Medicine with conflicting interpretations

Location: France  Primary collection method: clinical testing
Minimum review status of the submission from Department of Genetics, Rouen University Hospital, Normandy Center for Genomic and Personalized Medicine: Collection method of the submission from Department of Genetics, Rouen University Hospital, Normandy Center for Genomic and Personalized Medicine:
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
681 66 0 38 12 0 21 64

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 Genetics, Rouen University Hospital, Normandy Center for Genomic and Personalized Medicine pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 0 15 1 0 0
likely pathogenic 23 0 12 0 0
uncertain significance 6 3 0 3 2
likely benign 1 0 8 0 0

Submitter to submitter summary #

Total submitters: 53
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 16 0 6 6 0 10 22
GeneDx 0 24 0 5 3 0 4 12
OMIM 0 21 0 7 0 0 0 7
CeGaT Center for Human Genetics Tuebingen 0 8 0 3 2 0 2 7
Baylor Genetics 0 10 0 5 0 0 0 5
PreventionGenetics, part of Exact Sciences 0 3 0 0 2 0 1 3
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute 0 6 0 3 0 0 0 3
Institute of Human Genetics, University of Leipzig Medical Center 0 9 0 3 0 0 0 3
Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein 0 1 0 2 1 0 0 3
Revvity Omics, Revvity 0 4 0 1 0 0 1 2
Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München 0 3 0 2 0 0 0 2
Service de Génétique Moléculaire, Hôpital Robert Debré 0 1 0 2 0 0 0 2
Undiagnosed Diseases Network, NIH 0 1 0 2 0 0 0 2
Laboratoire de Génétique Moléculaire, CHU Bordeaux 0 2 0 1 0 0 1 2
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen 0 2 0 0 1 0 1 2
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen 0 4 0 1 0 0 1 2
Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City 0 0 0 2 0 0 0 2
Génétique des Maladies du Développement, Hospices Civils de Lyon 0 3 0 2 0 0 0 2
3billion 0 6 0 2 0 0 0 2
Genetics Laboratory, UDIAT-Centre Diagnòstic, Hospital Universitari Parc Tauli 0 2 0 2 0 0 0 2
Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center 0 4 0 0 0 0 1 1
Genetic Services Laboratory, University of Chicago 0 6 0 0 1 0 0 1
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine 0 1 0 1 0 0 0 1
Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital 0 0 0 1 0 0 0 1
Genome Diagnostics Laboratory, University Medical Center Utrecht 0 0 0 1 0 0 0 1
Fulgent Genetics, Fulgent Genetics 0 1 0 1 0 0 0 1
Department of Molecular and Human Genetics, Baylor College of Medicine 0 0 0 1 0 0 0 1
University of Washington Center for Mendelian Genomics, University of Washington 0 0 0 1 0 0 0 1
Laboratory of Molecular Genetics (Pr. Bezieau's lab), CHU de Nantes 0 1 0 0 0 0 1 1
Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden 0 2 0 0 0 0 1 1
Gene Discovery Core-Manton Center, Boston Children's Hospital 0 0 0 0 0 0 1 1
Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin 0 0 0 1 0 0 0 1
Diagnostic Laboratory, Strasbourg University Hospital 0 1 0 1 0 0 0 1
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ 0 2 0 1 0 0 0 1
Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India 0 2 0 0 0 0 1 1
Equipe Genetique des Anomalies du Developpement, Université de Bourgogne 0 4 0 1 0 0 0 1
SIB Swiss Institute of Bioinformatics 0 1 0 1 0 0 0 1
Geisinger Autism and Developmental Medicine Institute, Geisinger Health System 0 0 0 0 0 0 1 1
Sharon lab, Hadassah-Hebrew University Medical Center 0 0 0 1 0 0 0 1
Wong Mito Lab, Molecular and Human Genetics, Baylor College of Medicine 0 2 0 1 0 0 0 1
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) 0 0 0 0 1 0 0 1
Genetics Laboratory - UDIAT Centre Diagnòstic, Hospital Universitari Parc Tauli 0 0 0 1 0 0 0 1
Zotz-Klimas Genetics Lab, MVZ Zotz Klimas 0 1 0 1 0 0 0 1
Genomics Facility, Ludwig-Maximilians-Universität München 0 0 0 1 0 0 0 1
Clinical Genomics Program, Stanford Medicine 0 1 0 1 0 0 0 1
New York Genome Center 0 0 0 0 1 0 0 1
Genome-Nilou Lab 0 3 0 1 0 0 0 1
Arnesen Lab, University of Bergen 0 0 0 1 0 0 0 1
Molecular Genetics Lab, CHRU Brest 0 0 0 1 0 0 0 1
GenomeConnect - Simons Searchlight 0 1 0 1 0 0 0 1
Institute of Human Genetics, Clinical Exome/Genome Diagnostics Group, University Hospital Bonn 0 1 0 1 0 0 0 1
Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center 0 0 0 0 0 0 1 1
Cell and Gene Engineering Laboratory, Zhejiang University 0 0 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 64
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_004608.4(TBX6):c.484G>A (p.Gly162Ser) rs56098093 0.00404
NM_020066.5(FMN2):c.4619C>T (p.Ser1540Leu) rs150801382 0.00221
NM_002693.3(POLG):c.2243G>C (p.Trp748Ser) rs113994097 0.00081
NM_004608.4(TBX6):c.815G>A (p.Arg272Gln) rs201231713 0.00078
NM_022124.6(CDH23):c.7823G>A (p.Arg2608His) rs202052174 0.00059
NM_006767.4(LZTR1):c.264-13G>A rs587777176 0.00017
NM_000489.6(ATRX):c.3527A>T (p.Lys1176Met) rs191563592 0.00009
NM_005908.4(MANBA):c.1922G>A (p.Arg641His) rs569997475 0.00006
NM_001278716.2(FBXL4):c.64C>T (p.Arg22Ter) rs200440128 0.00005
NM_006180.6(NTRK2):c.2374C>T (p.Arg792Cys) rs201902834 0.00004
NM_002354.3(EPCAM):c.556-14A>G rs376155665 0.00003
NM_001375524.1(TRRAP):c.4079C>T (p.Pro1360Leu) rs139426093 0.00001
NM_001673.5(ASNS):c.1439C>T (p.Ser480Phe) rs754043007 0.00001
NM_004722.4(AP4M1):c.1137+1G>T rs770705832 0.00001
NM_000180.3(GUCY2D):c.389del (p.Pro130Leufs) rs61749670
NM_000702.4(ATP1A2):c.2723G>A (p.Arg908Gln) rs2101996488
NM_000827.4(GRIA1):c.1906G>A (p.Ala636Thr) rs587776937
NM_001005273.3(CHD3):c.3515G>A (p.Arg1172Gln) rs1567861501
NM_001029896.2(WDR45):c.827+2dup rs1602537729
NM_001032221.6(STXBP1):c.416C>T (p.Pro139Leu) rs796053353
NM_001040142.2(SCN2A):c.4904G>A (p.Arg1635Gln) rs1057520844
NM_001172509.2(SATB2):c.1174G>C (p.Gly392Arg) rs1688108689
NM_001172509.2(SATB2):c.597+1G>A rs1559016679
NM_001256012.3(MYH10):c.5681G>A (p.Arg1894Gln) rs1038557470
NM_001282534.2(KCNK9):c.392G>A (p.Arg131His) rs867543866
NM_001303052.2(MYT1L):c.1585G>A (p.Gly529Arg) rs1275489527
NM_001303256.3(MORC2):c.394C>T (p.Arg132Cys) rs1064795559
NM_001371928.1(AHDC1):c.1003G>A (p.Asp335Asn) rs1202158646
NM_001375524.1(TRRAP):c.5596C>T (p.Arg1866Cys) rs1791432323
NM_001376.5(DYNC1H1):c.2971A>G (p.Met991Val) rs1057518524
NM_001904.4(CTNNB1):c.1981C>T (p.Arg661Ter) rs748294403
NM_002074.5(GNB1):c.239T>C (p.Ile80Thr) rs752746786
NM_003042.4(SLC6A1):c.889G>A (p.Gly297Arg) rs876657400
NM_003073.5(SMARCB1):c.214dup (p.Thr72fs)
NM_003106.4(SOX2):c.368A>G (p.Asp123Gly) rs1249553271
NM_003491.4(NAA10):c.235C>T (p.Arg79Cys) rs1057524031
NM_004187.5(KDM5C):c.1439C>T (p.Pro480Leu) rs1057518697
NM_004859.4(CLTC):c.2669C>T (p.Pro890Leu)
NM_005629.4(SLC6A8):c.1171C>T (p.Arg391Trp) rs1557045267
NM_006086.4(TUBB3):c.136C>T (p.Arg46Trp) rs1555625363
NM_006236.3(POU3F3):c.1303_1305del (p.Glu435del)
NM_006516.4(SLC2A1):c.274C>T (p.Arg92Trp) rs202060209
NM_006772.3(SYNGAP1):c.388-3C>G rs1448169616
NM_007118.4(TRIO):c.3232C>T (p.Arg1078Trp)
NM_007325.5(GRIA3):c.2098G>A (p.Glu700Lys) rs2045826576
NM_007327.4(GRIN1):c.2500G>C (p.Glu834Gln) rs1588735834
NM_012199.5(AGO1):c.536TCT[1] (p.Phe180del) rs1553154062
NM_014423.4(AFF4):c.758C>T (p.Pro253Leu)
NM_015001.3(SPEN):c.2417_2418dup (p.Arg807fs) rs764595221
NM_015570.4(AUTS2):c.1603_1626del (p.531HQHT[1]) rs1789934246
NM_016373.4(WWOX):c.689A>C (p.Gln230Pro)
NM_016604.4(KDM3B):c.3871T>C (p.Ser1291Pro) rs2126994153
NM_016955.4(SEPSECS):c.114+3A>G
NM_020338.4(ZMIZ1):c.253C>T (p.Arg85Ter) rs1039220588
NM_020699.4(GATAD2B):c.1432C>T (p.Arg478Ter) rs761820222
NM_021008.4(DEAF1):c.646A>G (p.Lys216Glu) rs1590017652
NM_022455.5(NSD1):c.4378+3_4378+6del rs1562251194
NM_030665.4(RAI1):c.176A>G (p.Tyr59Cys) rs1240460489
NM_052867.4(NALCN):c.3959C>T (p.Thr1320Met)
NM_078480.3(PUF60):c.1673_1674del (p.Ser558fs) rs1816304706
NM_130839.5(UBE3A):c.2567_2570del (p.Lys856fs)
NM_133433.4(NIPBL):c.-467C>T rs1251456909
NM_138927.4(SON):c.5753_5756del (p.Val1918fs) rs886039773
NM_177559.3(CSNK2A1):c.593A>G (p.Lys198Arg) rs869312840

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