ClinVar Miner

Variants from Génétique des Maladies du Développement, Hospices Civils de Lyon with conflicting interpretations

Location: France  Primary collection method: clinical testing
Minimum review status of the submission from Génétique des Maladies du Développement, Hospices Civils de Lyon: Collection method of the submission from Génétique des Maladies du Développement, Hospices Civils de Lyon:
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
472 97 0 72 7 1 30 102

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
Génétique des Maladies du Développement, Hospices Civils de Lyon pathogenic likely pathogenic uncertain significance likely benign benign protective other
pathogenic 0 56 10 1 1 1 1
likely pathogenic 16 0 15 0 0 0 0
uncertain significance 2 2 0 1 1 0 0
likely benign 0 1 4 0 0 0 0
benign 0 0 1 0 0 0 0

Submitter to submitter summary #

Total submitters: 94
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 62 0 8 3 0 9 20
Institute of Human Genetics, University of Leipzig Medical Center 0 24 0 11 0 0 3 14
GeneDx 0 30 0 6 2 0 5 12
Revvity Omics, Revvity 0 7 0 1 2 0 3 6
Genetic Services Laboratory, University of Chicago 0 9 0 4 0 0 1 5
Eurofins Ntd Llc (ga) 0 3 0 2 0 1 4 5
CeGaT Center for Human Genetics Tuebingen 0 15 0 2 1 0 2 5
Equipe Genetique des Anomalies du Developpement, Université de Bourgogne 0 4 0 5 0 0 1 5
Baylor Genetics 0 19 0 4 0 0 0 4
Illumina Laboratory Services, Illumina 0 5 0 3 0 0 2 4
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ 0 5 0 3 1 0 0 4
Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego 0 5 0 3 0 0 1 4
SIB Swiss Institute of Bioinformatics 0 3 0 3 0 0 1 4
Athena Diagnostics Inc 0 2 0 3 0 0 1 3
PreventionGenetics, part of Exact Sciences 0 4 0 1 0 0 2 3
MGZ Medical Genetics Center 0 4 0 3 0 0 0 3
Genome Diagnostics Laboratory, University Medical Center Utrecht 0 4 0 3 0 0 0 3
Mendelics 0 3 0 2 0 0 1 3
University of Washington Center for Mendelian Genomics, University of Washington 0 0 0 3 0 0 0 3
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen 0 4 0 3 0 0 0 3
3billion 0 16 0 3 0 0 0 3
Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center 0 3 0 2 0 0 1 3
Genomics England Pilot Project, Genomics England 0 3 0 3 0 0 0 3
OMIM 0 45 0 2 0 0 0 2
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine 0 0 0 1 0 0 1 2
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories 0 0 0 2 0 0 0 2
Ambry Genetics 0 0 0 0 1 0 1 2
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute 0 11 0 2 0 0 0 2
Blueprint Genetics 0 1 0 2 0 0 0 2
Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics 0 1 0 1 0 0 1 2
Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden 0 1 0 1 0 0 1 2
Centre de Biologie Pathologie Génétique, Centre Hospitalier Universitaire de Lille 0 3 0 2 0 0 0 2
NIHR Bioresource Rare Diseases, University of Cambridge 0 0 0 2 0 0 0 2
Undiagnosed Diseases Network, NIH 0 3 0 2 0 0 1 2
Laboratoire de Genetique Moleculaire, Centre Hospitalier Universitaire de Bordeaux 0 0 0 1 0 0 1 2
Department of Genetics, Rouen University Hospital, Normandy Center for Genomic and Personalized Medicine 0 3 0 2 0 0 0 2
New York Genome Center 0 6 0 2 0 0 1 2
Institute of Human Genetics, Clinical Exome/Genome Diagnostics Group, University Hospital Bonn 0 0 0 2 0 0 0 2
Neuberg Centre For Genomic Medicine, NCGM 0 12 0 2 0 0 0 2
Institute of Human Genetics, University of Goettingen 0 0 0 1 0 0 0 1
Molecular Diagnostics Lab, Nemours Children's Health, Delaware 0 0 0 1 0 0 0 1
Institute for Genomic Medicine (IGM) Clinical Laboratory, Nationwide Children's Hospital 0 0 0 1 0 0 0 1
Elsea Laboratory, Baylor College of Medicine 0 1 0 1 0 0 0 1
Courtagen Diagnostics Laboratory, Courtagen Life Sciences 0 1 0 1 0 0 0 1
Counsyl 0 0 0 1 0 0 0 1
Mayo Clinic Laboratories, Mayo Clinic 0 1 0 1 0 0 1 1
Fulgent Genetics, Fulgent Genetics 0 11 0 1 0 0 0 1
Quest Diagnostics Nichols Institute San Juan Capistrano 0 0 0 0 0 0 1 1
ClinVar Staff, National Center for Biotechnology Information (NCBI) 0 0 0 1 0 0 0 1
Department Of Translational Genomics (developmental Genetics Section), King Faisal Specialist Hospital & Research Centre 0 0 0 1 0 0 0 1
UCLA Clinical Genomics Center, UCLA 0 2 0 1 0 0 0 1
Center for Medical Genetics Ghent, University of Ghent 0 0 0 1 0 0 0 1
Vavilov Institute of General Genetics RAS, Laboratory of Evolutional Genomics 0 0 0 0 0 1 0 1
Knight Diagnostic Laboratories, Oregon Health and Sciences University 0 0 0 1 0 0 0 1
Lupski Lab, Baylor-Hopkins CMG, Baylor College of Medicine 0 0 0 1 0 0 1 1
NeuroMeGen, Hospital Clinico Santiago de Compostela 0 1 0 1 0 0 0 1
Genome Sciences Centre, British Columbia Cancer Agency 0 0 0 1 0 0 0 1
Diagnostics Division, CENTRE FOR DNA FINGERPRINTING AND DIAGNOSTICS 0 0 0 1 0 0 0 1
Prof. Thelma's Laboratory, Department of Genetics, University of Delhi South Campus 0 0 0 1 0 0 0 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 0 0 0 1 1
Center for Statistical Genetics, Columbia University 0 0 0 0 0 0 1 1
Centre for Mendelian Genomics, University Medical Centre Ljubljana 0 3 0 1 0 0 0 1
Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India 0 4 0 1 0 0 0 1
Center for Molecular Medicine, Children’s Hospital of Fudan University 0 0 0 1 0 0 0 1
Department of Pathology and Laboratory Medicine, Sinai Health System 0 0 0 0 0 0 1 1
Geisinger Autism and Developmental Medicine Institute, Geisinger Health System 0 1 0 1 0 0 1 1
Rare Disease Group, Clinical Genetics, Karolinska Institutet 0 0 0 1 0 0 1 1
Institute of Cellular and Molecular Medicine, Copenhagen University 0 0 0 1 0 0 0 1
Genetics Department, University Hospital of Toulouse 0 0 0 1 0 0 0 1
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago 0 3 0 1 0 0 0 1
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen 0 3 0 0 1 0 0 1
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) 0 1 0 0 0 0 1 1
Genome Diagnostics Laboratory, Amsterdam University Medical Center 0 3 0 1 0 0 0 1
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center 0 1 0 0 0 0 1 1
Medical Genetics Lab, Policlinico S. Orsola.Malpighi 0 0 0 1 0 0 1 1
Medical Cytogenetics and Molecular Genetics Laboratory, IRCCS Istituto Auxologico Italiano 0 0 0 0 0 0 1 1
Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard 0 4 0 1 0 0 0 1
Laboratory of Medical Genetics, National & Kapodistrian University of Athens 0 3 0 1 0 0 0 1
Molecular Pathology Diagnostics Labratory, University of Iowa Hospitals & Clinics 0 0 0 1 0 0 0 1
Biochemistry Laboratory of CDMU, Chengde Medical University 0 0 0 1 0 0 0 1
Institute for Human Genetics, University Hospital Essen 0 0 0 1 0 0 0 1
Cytoplasmic Inheritance Laboratory, Institute of Genetics and Cytology 0 0 0 1 0 0 0 1
Zotz-Klimas Genetics Lab, MVZ Zotz Klimas 0 2 0 0 0 0 1 1
Clinical Genomics Program, Stanford Medicine 0 1 0 1 0 0 0 1
Rare Disease Group, University of Exeter 0 0 0 1 0 0 0 1
Genetics and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University 0 1 0 1 0 0 0 1
Pediatric Genetics Clinic, Sheba Medical Center 0 4 0 1 0 0 0 1
ClinGen Rett and Angelman-like Disorders Variant Curation Expert Panel 0 2 0 0 0 0 1 1
IU Genetic Testing Laboratories, Indiana University School of Medicine 0 0 0 1 0 0 0 1
Department of Neurology, Children’s Hospital of Chongqing Medical University 0 0 0 1 0 0 0 1
Chao Lab, Baylor College of Medicine, Texas Children's Hospital 0 0 0 1 0 0 0 1
Clinical Laboratory Sciences Program (CLSP), King Saud bin Abdulaziz University for Health Sciences (KSAU-HS) 0 2 0 1 0 0 0 1
Centre for Population Genomics, CPG 0 3 0 0 0 0 1 1

All variants with conflicting interpretations #

Total variants: 102
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_024570.4(RNASEH2B):c.529G>A (p.Ala177Thr) rs75184679 0.00141
NM_006567.5(FARS2):c.667C>T (p.Arg223Cys) rs202060864 0.00028
NM_001182.5(ALDH7A1):c.1279G>C (p.Glu427Gln) rs121912707 0.00024
NM_213622.4(STAMBP):c.112C>T (p.Arg38Cys) rs143739249 0.00009
NM_032178.3(SLC7A6OS):c.191A>G (p.Gln64Arg) rs190706099 0.00006
NM_001110792.2(MECP2):c.1250C>T (p.Pro417Leu) rs61753016 0.00004
NM_005055.5(RAPSN):c.848T>C (p.Leu283Pro) rs104894293 0.00004
NM_000334.4(SCN4A):c.3466G>A (p.Ala1156Thr) rs80338958 0.00003
NM_012123.4(MTO1):c.1282G>A (p.Ala428Thr) rs143747297 0.00003
NM_001037.5(SCN1B):c.373C>T (p.Arg125Cys) rs1135401736 0.00001
NM_006516.4(SLC2A1):c.277C>T (p.Arg93Trp) rs267607061 0.00001
NM_000382.3(ALDH3A2):c.798+5G>A
NM_000836.4(GRIN2D):c.2008C>T (p.Leu670Phe) rs1600982189
NM_000937.5(POLR2A):c.1462G>A (p.Val488Met) rs2070561031
NM_001005273.3(CHD3):c.3515G>A (p.Arg1172Gln) rs1567861501
NM_001029896.2(WDR45):c.397C>T (p.Arg133Ter) rs797046101
NM_001040142.2(SCN2A):c.1399G>T (p.Ala467Ser) rs745774658
NM_001040142.2(SCN2A):c.3956G>A (p.Arg1319Gln)
NM_001040142.2(SCN2A):c.4886G>A (p.Arg1629His)
NM_001040142.2(SCN2A):c.4976C>T (p.Ala1659Val) rs1060503101
NM_001040142.2(SCN2A):c.5317G>A (p.Ala1773Thr) rs796053162
NM_001040142.2(SCN2A):c.605C>T (p.Ala202Val)
NM_001099922.3(ALG13):c.320A>G (p.Asn107Ser) rs398122394
NM_001110556.2(FLNA):c.7628G>A (p.Cys2543Tyr)
NM_001110792.2(MECP2):c.509C>T (p.Thr170Met) rs28934906
NM_001110792.2(MECP2):c.535C>T (p.Arg179Trp) rs61748420
NM_001127222.2(CACNA1A):c.2134G>A (p.Ala712Thr)
NM_001127222.2(CACNA1A):c.4043G>A (p.Arg1348Gln) rs1057520918
NM_001127222.2(CACNA1A):c.4072C>T (p.Arg1358Trp) rs1555745461
NM_001127222.2(CACNA1A):c.6466C>G (p.Arg2156Gly) rs554393704
NM_001127644.2(GABRA1):c.335G>A (p.Arg112Gln) rs587777308
NM_001134407.3(GRIN2A):c.1362del (p.Lys454fs)
NM_001134407.3(GRIN2A):c.2146G>A (p.Ala716Thr)
NM_001161352.2(KCNMA1):c.2572C>T (p.Arg858Trp) rs199681253
NM_001165963.4(SCN1A):c.4324G>T (p.Val1442Phe) rs1690574155
NM_001165963.4(SCN1A):c.4582-2A>G rs2105449932
NM_001165963.4(SCN1A):c.5066T>C (p.Met1689Thr)
NM_001165963.4(SCN1A):c.602+1G>A
NM_001172509.2(SATB2):c.597+1G>A rs1559016679
NM_001184880.2(PCDH19):c.462C>G (p.Tyr154Ter) rs1569315876
NM_001271.4(CHD2):c.2095C>T (p.Arg699Trp)
NM_001271.4(CHD2):c.3112C>T (p.Arg1038Cys)
NM_001321075.3(DLG4):c.1083G>A (p.Ser361=) rs1227093654
NM_001323289.2(CDKL5):c.1675C>T (p.Arg559Ter) rs267608395
NM_001323289.2(CDKL5):c.2276+1G>A rs1602292181
NM_001330260.2(SCN8A):c.2549G>A (p.Arg850Gln)
NM_001330260.2(SCN8A):c.3967G>A (p.Ala1323Thr) rs794727361
NM_001330260.2(SCN8A):c.4115A>G (p.Asn1372Ser) rs2138904379
NM_001348323.3(TRIP12):c.5801C>T (p.Pro1934Leu)
NM_001352027.3(PHF21A):c.1741C>T (p.Arg581Ter)
NM_001353921.2(ARHGEF9):c.331C>T (p.Arg111Trp)
NM_001356.5(DDX3X):c.1595C>T (p.Thr532Met) rs1064795387
NM_001366145.2(TRPM3):c.3004G>A (p.Val1002Met) rs1564493599
NM_001370100.5(ZMYND11):c.1798C>T (p.Arg600Trp) rs797044854
NM_001904.4(CTNNB1):c.1759C>T (p.Arg587Ter) rs1064796453
NM_001958.5(EEF1A2):c.364G>A (p.Glu122Lys)
NM_002074.5(GNB1):c.239T>C (p.Ile80Thr) rs752746786
NM_002074.5(GNB1):c.284T>C (p.Leu95Pro) rs869312824
NM_002397.5(MEF2C):c.44G>A (p.Arg15His) rs1202957297
NM_002641.4(PIGA):c.356G>A (p.Arg119Gln)
NM_002653.5(PITX1):c.793G>T (p.Gly265Cys) rs141612135
NM_003748.4(ALDH4A1):c.1571G>A (p.Arg524Gln)
NM_004113.6(FGF12):c.155G>A (p.Arg52His) rs886039903
NM_004415.4(DSP):c.1783C>T (p.Gln595Ter)
NM_004519.4(KCNQ3):c.689G>A (p.Arg230His)
NM_004519.4(KCNQ3):c.956A>G (p.Tyr319Cys) rs1554627218
NM_004974.4(KCNA2):c.1214C>T (p.Pro405Leu)
NM_004975.4(KCNB1):c.1297C>T (p.Arg433Ter) rs1064794764
NM_004975.4(KCNB1):c.934C>T (p.Arg312Cys)
NM_005445.4(SMC3):c.181C>T (p.Arg61Trp) rs866273473
NM_006245.4(PPP2R5D):c.592G>A (p.Glu198Lys)
NM_006772.3(SYNGAP1):c.928G>A (p.Glu310Lys) rs1554121206
NM_006908.5(RAC1):c.116A>G (p.Asn39Ser)
NM_006914.4(RORB):c.1163T>A (p.Ile388Asn)
NM_006940.6(SOX5):c.1711C>T (p.Arg571Trp) rs1565669640
NM_007144.3(PCGF2):c.194C>T (p.Pro65Leu)
NM_007325.5(GRIA3):c.1236A>C (p.Gln412His) rs2045454194
NM_012309.5(SHANK2):c.2439+1G>A rs2058899044
NM_012479.4(YWHAG):c.394C>T (p.Arg132Cys) rs1554616628
NM_014225.6(PPP2R1A):c.656C>T (p.Ser219Leu) rs1555791268
NM_014225.6(PPP2R1A):c.773G>A (p.Arg258His) rs863225094
NM_015047.3(EMC1):c.1134C>A (p.Tyr378Ter) rs778470143
NM_015047.3(EMC1):c.2858T>C (p.Phe953Ser) rs1267383375
NM_015267.4(CUX2):c.1768G>A (p.Glu590Lys)
NM_016373.4(WWOX):c.689A>C (p.Gln230Pro)
NM_018026.4(PACS1):c.607C>T (p.Arg203Trp) rs398123009
NM_018486.3(HDAC8):c.1081C>T (p.Arg361Ter) rs1555948969
NM_020137.5(GRIPAP1):c.1669G>A (p.Glu557Lys)
NM_020822.3(KCNT1):c.1421G>A (p.Arg474His)
NM_020822.3(KCNT1):c.2798G>A (p.Arg933His) rs1023136319
NM_020822.3(KCNT1):c.2849G>A (p.Arg950Gln)
NM_020988.3(GNAO1):c.118G>C (p.Gly40Arg) rs886041715
NM_020988.3(GNAO1):c.680C>T (p.Ala227Val)
NM_020988.3(GNAO1):c.904G>A (p.Ala302Thr) rs2143704776
NM_022552.5(DNMT3A):c.1004A>G (p.Lys335Arg) rs2149307214
NM_130839.5(UBE3A):c.2567_2570del (p.Lys856fs)
NM_145239.3(PRRT2):c.649dup (p.Arg217fs)
NM_152296.5(ATP1A3):c.1825G>T (p.Asp609Tyr)
NM_170675.5(MEIS2):c.934_937del (p.Leu312fs) rs1595790647
NM_172107.4(KCNQ2):c.1657C>T (p.Arg553Trp) rs759584387
NM_172107.4(KCNQ2):c.638G>A (p.Arg213Gln)
Single allele

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