ClinVar Miner

Variants from Centre de Biologie Pathologie Génétique, Centre Hospitalier Universitaire de Lille with conflicting interpretations

Location: France  Primary collection method: clinical testing
Minimum review status of the submission from Centre de Biologie Pathologie Génétique, Centre Hospitalier Universitaire de Lille: Collection method of the submission from Centre de Biologie Pathologie Génétique, Centre Hospitalier Universitaire de Lille:
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
1388 117 0 89 3 0 22 109

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
Centre de Biologie Pathologie Génétique, Centre Hospitalier Universitaire de Lille pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 0 65 4 0 0
likely pathogenic 25 0 16 1 0
uncertain significance 1 2 0 1 1
likely benign 0 0 1 0 1

Submitter to submitter summary #

Total submitters: 81
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 59 0 12 0 0 5 17
Labcorp Genetics (formerly Invitae), Labcorp 0 42 0 7 0 0 5 12
3billion 0 30 0 8 0 0 1 9
CeGaT Center for Human Genetics Tuebingen 0 29 0 4 0 0 2 6
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute 0 19 0 4 0 0 1 5
Fulgent Genetics, Fulgent Genetics 0 10 0 2 0 0 2 4
Institute of Human Genetics Munich, TUM University Hospital 0 12 0 4 0 0 0 4
Institute of Human Genetics, University of Leipzig Medical Center 0 15 0 4 0 0 0 4
OMIM 0 37 0 4 0 0 0 4
Solve-RD Consortium 0 1 0 4 0 0 0 4
Cambridge Genomics Laboratory, East Genomic Laboratory Hub, NHS Genomic Medicine Service 0 4 0 1 2 0 0 3
Eurofins Ntd Llc (ga) 0 12 0 1 0 0 2 3
Genome-Nilou Lab 0 2 0 3 0 0 0 3
MGZ Medical Genetics Center 0 5 0 3 0 0 0 3
PreventionGenetics, part of Exact Sciences 0 14 0 1 1 0 1 3
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 0 13 0 2 0 0 1 3
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital 0 1 0 1 0 0 1 2
Centre de Biologie Pathologie Génétique, Centre Hospitalier Universitaire de Lille 1612 0 0 2 0 0 0 2
Division Of Personalized Genomic Medicine, Columbia University Irving Medical Center 0 0 0 2 0 0 0 2
Genetics Laboratory, Great Ormond Street Hospital NHS Foundation Trust, North Thames Genomic Laboratory Hub 0 1 0 1 0 0 1 2
Genetics Laboratory, UDIAT-Centre Diagnòstic, Hospital Universitari Parc Tauli 0 3 0 2 0 0 0 2
Génétique des Maladies du Développement, Hospices Civils de Lyon 0 6 0 2 0 0 0 2
Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India 0 4 0 2 0 0 0 2
Medical and Scientific Branch, Hong Kong Genome Institute 0 0 0 2 0 0 0 2
Mendelics 0 7 0 2 0 0 0 2
Molecular Diagnostics Lab, Nemours Children's Health, Delaware 0 1 0 1 0 0 1 2
Molecular Genetics Department, Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology 0 0 0 2 0 0 0 2
Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego 0 8 0 2 0 0 0 2
SIB Swiss Institute of Bioinformatics 0 0 0 2 0 0 0 2
University of Washington Center for Mendelian Genomics, University of Washington 0 0 0 2 0 0 0 2
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories 0 9 0 0 0 0 1 1
Athena Diagnostics 0 5 0 1 0 0 0 1
Autoinflammatory diseases unit, CHU de Montpellier 0 1 0 1 0 0 0 1
Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City 0 3 0 1 0 0 0 1
Center for Human Genetics, Inc, Center for Human Genetics, Inc 0 3 0 0 0 0 1 1
Center for Human Genetics, University of Leuven 0 0 0 1 0 0 0 1
Center of Human Genetics, Hôpital Erasme 0 4 0 1 0 0 0 1
Centre for Population Genomics, CPG 0 2 0 1 0 0 0 1
ClinVar Staff, National Center for Biotechnology Information (NCBI) 0 0 0 1 0 0 0 1
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center 0 7 0 1 0 0 0 1
Clinical Genetics Laboratory, University Hospital Schleswig-Holstein 0 3 0 1 0 0 0 1
Counsyl 0 0 0 1 0 0 0 1
Department of Genetics, Rouen University Hospital, Normandy Center for Genomic and Personalized Medicine 0 3 0 1 0 0 0 1
Department of Pathology and Laboratory Medicine, Sinai Health System 0 1 0 0 0 0 1 1
Diagnostic Laboratory, Strasbourg University Hospital 0 0 0 0 0 0 1 1
Equipe Genetique des Anomalies du Developpement, Université de Bourgogne 0 10 0 1 0 0 0 1
Genetic Services Laboratory, University of Chicago 0 11 0 0 0 0 1 1
Genome Diagnostics Laboratory, Amsterdam University Medical Center 0 7 0 1 0 0 0 1
Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre 0 8 0 1 0 0 0 1
Genomic Medicine Lab, University of California San Francisco 0 0 0 1 0 0 0 1
Genomics England Pilot Project, Genomics England 0 0 0 1 0 0 0 1
Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center 0 10 0 1 0 0 0 1
HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology 0 4 0 1 0 0 0 1
Human Genetics, University of Luebeck 0 0 0 1 0 0 0 1
Institute for Human Genetics, University Hospital Essen 0 1 0 0 0 0 1 1
Institute of Human Genetics, Heidelberg University 0 0 0 1 0 0 0 1
Institute of Human Genetics, University Hospital of Duesseldorf 0 2 0 1 0 0 0 1
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen 0 13 0 1 0 0 0 1
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ 0 11 0 1 0 0 0 1
Juno Genomics, Hangzhou Juno Genomics, Inc 0 1 0 1 0 0 0 1
Laboratoire de Génétique Moléculaire Institut de Recherche Necker Enfants Malades, CHU Paris - Hôpital Necker-Enfants Malades 0 0 0 1 0 0 0 1
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine 0 1 0 1 0 0 0 1
Leiden Open Variation Database 0 0 0 0 0 0 1 1
Lupski Lab, Baylor-Hopkins CMG, Baylor College of Medicine 0 0 0 1 0 0 0 1
Mayo Clinic Laboratories, Mayo Clinic 0 8 0 0 1 0 0 1
Molecular Genetics Lab, CHRU Brest 0 1 0 1 0 0 0 1
Molecular Genetics Laboratory, BC Children's and BC Women's Hospitals 0 1 0 1 0 0 0 1
Molecular Genetics laboratory, Necker Hospital 0 3 0 1 0 0 0 1
NIHR Bioresource Rare Diseases, University of Cambridge 0 1 0 1 0 0 0 1
Natera, Inc. 0 1 0 1 0 0 0 1
Neonatal Intensive Care Unit, Fujian Provincial Hospital 0 0 0 1 0 0 0 1
Neuberg Centre For Genomic Medicine, NCGM 0 3 0 0 0 0 1 1
New York Genome Center 0 7 0 1 0 0 0 1
OLLIN Analises Genomicas, OLLIN 0 2 0 1 0 0 0 1
Precision Medicine Center, Zhengzhou University 0 0 0 1 0 0 0 1
RettBASE 0 4 0 1 0 0 0 1
Revvity Omics, Revvity 0 25 0 0 0 0 1 1
Tumer Group, Copenhagen University Hospital, Rigshospitalet 0 0 0 1 0 0 0 1
UCLA Clinical Genomics Center, UCLA 0 2 0 1 0 0 0 1
Undiagnosed Diseases Network, NIH 0 6 0 1 0 0 0 1
Variantyx, Inc. 0 8 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 109
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_015107.3(PHF8):c.2720G>A (p.Arg907His) rs142630105 0.00233
NM_001371986.1(UNC80):c.1806G>C (p.Gln602His) rs200473652 0.00163
NM_024063.3(AFG2B):c.527G>T (p.Gly176Val) rs145451123 0.00098
NM_016042.4(EXOSC3):c.395A>C (p.Asp132Ala) rs141138948 0.00048
NM_001383.6(DPH1):c.359T>C (p.Leu120Pro) rs200530055 0.00029
NM_001182.5(ALDH7A1):c.1279G>C (p.Glu427Gln) rs121912707 0.00023
NM_001082971.2(DDC):c.1435A>G (p.Arg479Gly) rs200450773 0.00015
NM_001271.4(CHD2):c.4984C>T (p.His1662Tyr) rs146275216 0.00006
NM_001127222.2(CACNA1A):c.5932G>A (p.Glu1978Lys) rs1266642291 0.00003
NM_001371986.1(UNC80):c.4544C>T (p.Ala1515Val) rs750442854 0.00003
NM_001673.5(ASNS):c.146G>A (p.Arg49Gln) rs769236847 0.00003
NM_001931.5(DLAT):c.976-1G>A rs367875541 0.00003
NM_020247.5(COQ8A):c.1228C>T (p.Arg410Ter) rs753254213 0.00003
NM_032043.3(BRIP1):c.2543G>A (p.Arg848His) rs374334794 0.00003
NM_001110556.2(FLNA):c.1966C>T (p.Leu656Phe) rs137853311 0.00002
NM_004539.4(NARS1):c.1564C>T (p.Arg522Ter) rs747737475 0.00002
NM_001005273.3(CHD3):c.5007_5008del (p.Asp1671fs) rs967826828 0.00001
NM_001134831.2(AHI1):c.2266G>T (p.Gly756Cys) rs376754552 0.00001
NM_002834.5(PTPN11):c.1492C>T (p.Arg498Trp) rs397507541 0.00001
NM_005121.3(MED13):c.5683_5684del (p.Met1895fs) rs750570850 0.00001
NM_015937.6(PIGT):c.1079G>T (p.Gly360Val) rs1277383877 0.00001
NM_018026.4(PACS1):c.607C>T (p.Arg203Trp) rs398123009 0.00001
NM_024063.3(AFG2B):c.2087G>T (p.Cys696Phe) rs747249958 0.00001
NM_057175.5(NAA15):c.239_240del (p.His80fs) rs779009256 0.00001
NM_181486.4(TBX5):c.710G>A (p.Arg237Gln) rs104894378 0.00001
NM_000188.3(HK1):c.1240G>A (p.Gly414Arg) rs2132871580
NM_000276.4(OCRL):c.940-11G>A rs776743373
NM_000314.8(PTEN):c.94ATT[1] (p.Ile33del) rs1554893765
NM_000474.4(TWIST1):c.309C>G (p.Tyr103Ter) rs104894054
NM_000489.6(ATRX):c.736C>T (p.Arg246Cys) rs122445105
NM_000814.6(GABRB3):c.358G>A (p.Asp120Asn) rs886037938
NM_000814.6(GABRB3):c.901C>T (p.Pro301Ser) rs1889966666
NM_001003694.2(BRPF1):c.2311+1G>A rs2077062359
NM_001007527.2(LMBRD2):c.1448G>A (p.Arg483His) rs2111857835
NM_001038.6(SCNN1A):c.1579TTC[1] (p.Phe528del) rs61759913
NM_001100.4(ACTA1):c.809G>A (p.Gly270Asp) rs1553255362
NM_001110556.2(FLNA):c.134A>G (p.Gln45Arg) rs398123613
NM_001110792.2(MECP2):c.1198_1208del (p.Pro399_Pro400insTer) rs2065919863
NM_001110792.2(MECP2):c.1240_1241insT (p.Pro414fs) rs2148659573
NM_001110792.2(MECP2):c.433C>T (p.Arg145Cys) rs28934904
NM_001110792.2(MECP2):c.437C>G (p.Ser146Cys) rs61748390
NM_001110792.2(MECP2):c.710C>G (p.Pro237Arg) rs61749715
NM_001110792.2(MECP2):c.916C>T (p.Arg306Ter) rs61751362
NM_001127222.2(CACNA1A):c.4291C>T (p.Arg1431Ter) rs1568470104
NM_001127222.2(CACNA1A):c.4988G>A (p.Arg1663Gln) rs121908247
NM_001165963.4(SCN1A):c.2927T>C (p.Met976Thr) rs1057518325
NM_001197104.2(KMT2A):c.478C>T (p.Arg160Ter) rs1555034779
NM_001292034.3(TAB2):c.679C>T (p.Arg227Ter) rs1479104927
NM_001303052.2(MYT1L):c.1516T>C (p.Cys506Arg) rs2052983721
NM_001321075.3(DLG4):c.1878C>A (p.Cys626Ter) rs1451196379
NM_001330260.2(SCN8A):c.5630A>G (p.Asn1877Ser) rs587780455
NM_001330288.2(SMARCC2):c.326dup (p.Tyr109Ter) rs2135750656
NM_001348323.3(TRIP12):c.4302_4303del (p.Tyr1435fs) rs2154259932
NM_001348716.2(KDM6B):c.1483C>T (p.Arg495Ter) rs1597842212
NM_001349338.3(FOXP1):c.1240_1241del (p.Leu414fs) rs1064793130
NM_001353345.2(SETD1B):c.5375G>A (p.Arg1792Gln) rs2137588997
NM_001356.5(DDX3X):c.874C>T (p.Arg292Ter) rs1555953488
NM_001371928.1(AHDC1):c.2062C>T (p.Arg688Ter) rs1165205177
NM_001376.5(DYNC1H1):c.791G>A (p.Arg264Gln) rs713993043
NM_001429.4(EP300):c.104_107del (p.Ser35fs) rs886037664
NM_002074.5(GNB1):c.239T>C (p.Ile80Thr) rs752746786
NM_002430.3(MN1):c.3744G>A (p.Trp1248Ter) rs1297805962
NM_002709.3(PPP1CB):c.146C>G (p.Pro49Arg) rs886037952
NM_002968.3(SALL1):c.2390del (p.Pro797fs)
NM_002968.3(SALL1):c.826C>T (p.Arg276Ter) rs104894537
NM_002968.3(SALL1):c.871C>T (p.Gln291Ter) rs1962424706
NM_003036.4(SKI):c.100G>A (p.Gly34Ser) rs387907306
NM_003042.4(SLC6A1):c.1084G>A (p.Gly362Arg) rs1131691302
NM_003482.4(KMT2D):c.16019G>A (p.Arg5340Gln) rs1565756106
NM_004380.3(CREBBP):c.3779+1G>C rs587783483
NM_004493.3(HSD17B10):c.439C>T (p.Arg147Cys) rs1064794694
NM_004975.4(KCNB1):c.968C>T (p.Thr323Ile) rs1569017257
NM_006245.4(PPP2R5D):c.592G>A (p.Glu198Lys) rs863225082
NM_006516.4(SLC2A1):c.376C>T (p.Arg126Cys) rs80359818
NM_006766.5(KAT6A):c.2218del (p.Arg740fs) rs1587723169
NM_006772.3(SYNGAP1):c.1685C>T (p.Pro562Leu) rs397514670
NM_006852.6(TLK2):c.1121+1G>A rs2146617330
NM_006852.6(TLK2):c.1550+1G>A rs2147105351
NM_006908.5(RAC1):c.116A>G (p.Asn39Ser) rs1554263624
NM_006940.6(SOX5):c.1678A>G (p.Met560Val) rs1591908609
NM_006950.3(SYN1):c.614T>A (p.Leu205Gln) rs2057892972
NM_007118.4(TRIO):c.4103A>G (p.Asp1368Gly) rs2152363791
NM_007118.4(TRIO):c.6153+1G>A rs1755124330
NM_007327.4(GRIN1):c.1858G>A (p.Gly620Arg) rs797045047
NM_007327.4(GRIN1):c.1921A>T (p.Met641Leu) rs2131299136
NM_013275.6(ANKRD11):c.2618_2619del (p.Val873fs) rs2034464059
NM_014233.4(UBTF):c.628G>A (p.Glu210Lys) rs1555582065
NM_015335.5(MED13L):c.2606C>T (p.Pro869Leu) rs1878458116
NM_015338.6(ASXL1):c.3700C>T (p.Gln1234Ter) rs1569337452
NM_015981.4(CAMK2A):c.329C>T (p.Ala110Val) rs779607303
NM_016604.4(KDM3B):c.4414C>T (p.Arg1472Ter) rs1561796122
NM_019597.5(HNRNPH2):c.616C>T (p.Arg206Trp) rs886039763
NM_020699.4(GATAD2B):c.1198_1199del (p.Ser400fs) rs1674480467
NM_021096.4(CACNA1I):c.1184T>A (p.Val395Asp) rs2146426462
NM_032271.3(TRAF7):c.1919T>C (p.Leu640Pro) rs2141299157
NM_032271.3(TRAF7):c.1964G>A (p.Arg655Gln) rs1331463984
NM_078480.3(PUF60):c.449_457del (p.Ala150_Phe152del) rs1131692232
NM_078480.3(PUF60):c.612_630del (p.Asn207fs) rs1816565452
NM_133330.3(NSD2):c.1676_1679del rs1553873247
NM_138927.4(SON):c.5753_5756del (p.Val1918fs) rs886039773
NM_145207.3(AFG2A):c.983CAA[2] (p.Thr330del) rs796052243
NM_145239.3(PRRT2):c.649dup (p.Arg217fs) rs587778771
NM_152564.5(VPS13B):c.8995-2A>G rs1554569259
NM_177559.3(CSNK2A1):c.466G>C (p.Asp156His) rs1568512728
NM_177559.3(CSNK2A1):c.593A>G (p.Lys198Arg) rs869312840
NM_181486.4(TBX5):c.1203G>A (p.Trp401Ter) rs377649723
NM_181486.4(TBX5):c.510+5G>A rs1555226301
NM_181486.4(TBX5):c.668C>T (p.Thr223Met) rs1555225344
NM_198904.4(GABRG2):c.373C>T (p.Arg125Cys) rs2113325423

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