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:
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
1399 98 0 66 2 0 25 89

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
pathogenic 0 47 6 1
likely pathogenic 19 0 16 1
uncertain significance 1 1 0 1
likely benign 0 0 1 0

Submitter to submitter summary #

Total submitters: 62
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 50 0 9 0 0 6 15
Invitae 0 36 0 6 0 0 5 11
CeGaT Center for Human Genetics Tuebingen 0 24 0 4 0 0 1 5
3billion 0 16 0 4 0 0 1 5
OMIM 0 33 0 4 0 0 0 4
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 0 7 0 2 0 0 2 4
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute 0 13 0 1 0 0 3 4
MGZ Medical Genetics Center 0 5 0 3 0 0 0 3
Eurofins Ntd Llc (ga) 0 12 0 1 0 0 2 3
Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München 0 11 0 3 0 0 0 3
Institute of Human Genetics, University of Leipzig Medical Center 0 13 0 3 0 0 0 3
Genome-Nilou Lab 0 2 0 3 0 0 0 3
Athena Diagnostics Inc 0 4 0 1 0 0 1 2
Molecular Diagnostics Lab, Nemours Children's Health, Delaware 0 1 0 1 0 0 1 2
PreventionGenetics, part of Exact Sciences 0 9 0 0 1 0 1 2
Fulgent Genetics, Fulgent Genetics 0 8 0 1 0 0 1 2
University of Washington Center for Mendelian Genomics, University of Washington 0 0 0 2 0 0 0 2
Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India 0 2 0 2 0 0 0 2
SIB Swiss Institute of Bioinformatics 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
New York Genome Center 0 8 0 1 1 0 0 2
Division Of Personalized Genomic Medicine, Columbia University Irving Medical Center 0 0 0 2 0 0 0 2
Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center 0 9 0 1 0 0 0 1
Center for Human Genetics, Inc, Center for Human Genetics, Inc 0 3 0 0 0 0 1 1
Genetic Services Laboratory, University of Chicago 0 10 0 0 0 0 1 1
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine 0 1 0 1 0 0 0 1
Molecular Genetics Laboratory, BC Children's and BC Women's Hospitals 0 0 0 1 0 0 0 1
Counsyl 0 0 0 1 0 0 0 1
Natera, Inc. 0 0 0 1 0 0 0 1
Mendelics 0 6 0 1 0 0 0 1
Quest Diagnostics Nichols Institute San Juan Capistrano 0 3 0 0 0 0 1 1
ClinVar Staff, National Center for Biotechnology Information (NCBI) 0 0 0 1 0 0 0 1
RettBASE 0 4 0 1 0 0 0 1
Illumina Laboratory Services, Illumina 0 10 0 0 0 0 1 1
UCLA Clinical Genomics Center, UCLA 0 2 0 1 0 0 0 1
HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology 0 4 0 1 0 0 0 1
Lupski Lab, Baylor-Hopkins CMG, Baylor College of Medicine 0 0 0 1 0 0 0 1
Center for Human Genetics, University of Leuven 0 0 0 1 0 0 0 1
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital 0 0 0 1 0 0 0 1
Diagnostic Laboratory, Strasbourg University Hospital 0 1 0 0 0 0 1 1
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ 0 11 0 1 0 0 0 1
Centre for Mendelian Genomics, University Medical Centre Ljubljana 0 2 0 1 0 0 0 1
Institute of Human Genetics, University Hospital of Duesseldorf 0 2 0 0 0 0 1 1
NIHR Bioresource Rare Diseases, University of Cambridge 0 2 0 1 0 0 0 1
Undiagnosed Diseases Network, NIH 0 5 0 1 0 0 0 1
Equipe Genetique des Anomalies du Developpement, Université de Bourgogne 0 10 0 1 0 0 0 1
Leiden Open Variation Database 0 0 0 0 0 0 1 1
Genome Diagnostics Laboratory, Amsterdam University Medical Center 0 7 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
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center 0 7 0 1 0 0 0 1
Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City 0 3 0 1 0 0 0 1
Marseille Medical Genetics, U1251, Aix Marseille University, Inserm 0 0 0 1 0 0 0 1
Institute for Human Genetics, University Hospital Essen 0 1 0 0 0 0 1 1
Autoinflammatory diseases unit, CHU de Montpellier 0 1 0 1 0 0 0 1
Molecular Genetics laboratory, Necker Hospital 0 3 0 1 0 0 0 1
Molecular Genetics Lab, CHRU Brest 0 1 0 1 0 0 0 1
Genetics Laboratory, UDIAT-Centre Diagnòstic, Hospital Universitari Parc Tauli 0 2 0 1 0 0 0 1
Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center 0 4 0 1 0 0 0 1
Genomics England Pilot Project, Genomics England 0 0 0 1 0 0 0 1
Human Genetics, University of Luebeck 0 0 0 1 0 0 0 1
Tumer Group, Copenhagen University Hospital, Rigshospitalet 0 0 0 1 0 0 0 1
Centre for Population Genomics, CPG 0 2 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 89
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
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_001383.6(DPH1):c.359T>C (p.Leu120Pro) rs200530055 0.00029
NM_001182.5(ALDH7A1):c.1279G>C (p.Glu427Gln) rs121912707 0.00024
NM_001082971.2(DDC):c.1435A>G (p.Arg479Gly) rs200450773 0.00016
NM_001371986.1(UNC80):c.4544C>T (p.Ala1515Val) rs750442854 0.00004
NM_001673.5(ASNS):c.146G>A (p.Arg49Gln) rs769236847 0.00004
NM_020247.5(COQ8A):c.1228C>T (p.Arg410Ter) rs753254213 0.00004
NM_001931.5(DLAT):c.976-1G>A rs367875541 0.00003
NM_032043.3(BRIP1):c.2543G>A (p.Arg848His) rs374334794 0.00003
NM_004539.4(NARS1):c.1564C>T (p.Arg522Ter) rs747737475 0.00002
NM_000528.4(MAN2B1):c.856G>A (p.Glu286Lys) rs772562587 0.00001
NM_001005273.3(CHD3):c.5007_5008del (p.Asp1671fs) rs967826828 0.00001
NM_001042492.3(NF1):c.5488C>T (p.Arg1830Cys) rs797045139 0.00001
NM_001110556.2(FLNA):c.1966C>T (p.Leu656Phe) rs137853311 0.00001
NM_001244008.2(KIF1A):c.4648C>T (p.Arg1550Trp) rs1468401006 0.00001
NM_003680.4(YARS1):c.176T>C (p.Ile59Thr) rs774466323 0.00001
NM_015937.6(PIGT):c.1079G>T (p.Gly360Val) rs1277383877 0.00001
NM_018297.4(NGLY1):c.931G>A (p.Glu311Lys) rs201791209 0.00001
NM_024063.3(AFG2B):c.2087G>T (p.Cys696Phe) rs747249958 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_000489.6(ATRX):c.736C>T (p.Arg246Cys) rs122445105
NM_000814.6(GABRB3):c.358G>A (p.Asp120Asn) rs886037938
NM_001007527.2(LMBRD2):c.1448G>A (p.Arg483His) rs2111857835
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.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.4988G>A (p.Arg1663Gln) rs121908247
NM_001165963.4(SCN1A):c.472G>C (p.Glu158Gln) rs796053090
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_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_003036.4(SKI):c.100G>A (p.Gly34Ser) rs387907306
NM_003042.4(SLC6A1):c.1084G>A (p.Gly362Arg) rs1131691302
NM_003042.4(SLC6A1):c.1531G>A (p.Val511Met) rs1064794981
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_004655.4(AXIN2):c.-12_8del (p.Met1fs) rs768265778
NM_004975.4(KCNB1):c.968C>T (p.Thr323Ile) rs1569017257
NM_005629.4(SLC6A8):c.1016+2T>C rs1557045066
NM_006015.6(ARID1A):c.4101G>A (p.Gln1367=) rs2081109271
NM_006245.4(PPP2R5D):c.592G>A (p.Glu198Lys)
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)
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_007327.4(GRIN1):c.1858G>A (p.Gly620Arg) rs797045047
NM_013275.6(ANKRD11):c.2618_2619del (p.Val873fs) rs2034464059
NM_014233.4(UBTF):c.628G>A (p.Glu210Lys) rs1555582065
NM_018026.4(PACS1):c.607C>T (p.Arg203Trp) rs398123009
NM_019597.5(HNRNPH2):c.616C>T (p.Arg206Trp) rs886039763
NM_020699.4(GATAD2B):c.1198_1199del (p.Ser400fs) rs1674480467
NM_078480.3(PUF60):c.449_457del (p.Ala150_Phe152del) rs1131692232
NM_078480.3(PUF60):c.612_630del (p.Asn207fs) rs1816565452
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)
NM_152296.5(ATP1A3):c.2438C>T (p.Ala813Val)
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.510+5G>A rs1555226301
NM_198904.4(GABRG2):c.373C>T (p.Arg125Cys) rs2113325423

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