ClinVar Miner

Variants from Laboratoire de Génétique Moléculaire, CHU Bordeaux with conflicting interpretations

Location: France  Primary collection method: clinical testing
Minimum review status of the submission from Laboratoire de Génétique Moléculaire, CHU Bordeaux: Collection method of the submission from Laboratoire de Génétique Moléculaire, CHU Bordeaux:
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
167 50 0 38 1 0 14 46

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
Laboratoire de Génétique Moléculaire, CHU Bordeaux pathogenic likely pathogenic uncertain significance
pathogenic 0 18 5
likely pathogenic 20 0 9
likely benign 0 0 1

Submitter to submitter summary #

Total submitters: 61
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 32 0 11 1 0 1 13
Invitae 0 22 0 6 0 0 3 9
OMIM 0 6 0 6 0 0 0 6
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 0 1 0 4 0 0 1 5
Eurofins Ntd Llc (ga) 0 6 0 4 1 0 0 5
CeGaT Center for Human Genetics Tuebingen 0 16 0 3 0 0 1 4
Institute of Human Genetics, University of Leipzig Medical Center 0 3 0 4 0 0 0 4
Athena Diagnostics Inc 0 5 0 2 1 0 0 3
Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center 0 4 0 2 0 0 1 3
Genetic Services Laboratory, University of Chicago 0 6 0 2 1 0 0 3
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine 0 1 0 3 0 0 0 3
Mendelics 0 1 0 2 0 0 1 3
Fulgent Genetics, Fulgent Genetics 0 2 0 3 0 0 0 3
Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden 0 3 0 2 1 0 0 3
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ 0 7 0 3 0 0 0 3
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen 0 5 0 3 0 0 0 3
Revvity Omics, Revvity 0 5 0 2 0 0 0 2
MGZ Medical Genetics Center 0 2 0 2 0 0 0 2
Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München 0 4 0 2 0 0 0 2
RettBASE 0 1 0 1 0 0 1 2
Illumina Laboratory Services, Illumina 0 3 0 2 0 0 0 2
Clinical Genomics Laboratory, Washington University in St. Louis 0 0 0 2 0 0 0 2
HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology 0 3 0 2 0 0 0 2
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center 0 8 0 2 0 0 0 2
Genomic Medicine Lab, University of California San Francisco 0 1 0 2 0 0 0 2
Department of Genetics, Rouen University Hospital, Normandy Center for Genomic and Personalized Medicine 0 2 0 1 0 0 1 2
3billion 0 4 0 2 0 0 0 2
Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet 0 0 0 1 0 0 0 1
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories 0 2 0 1 0 0 0 1
PreventionGenetics, part of Exact Sciences 0 8 0 1 0 0 0 1
Genome Diagnostics Laboratory, University Medical Center Utrecht 0 3 0 1 0 0 0 1
Counsyl 0 0 0 0 0 0 1 1
Mayo Clinic Laboratories, Mayo Clinic 0 3 0 1 0 0 0 1
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute 0 1 0 1 0 0 0 1
Laboratory of Molecular Genetics (Pr. Bezieau's lab), CHU de Nantes 0 1 0 1 0 0 0 1
Centre for Mendelian Genomics, University Medical Centre Ljubljana 0 1 0 0 0 0 1 1
Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India 0 1 0 1 0 0 0 1
Daryl Scott Lab, Baylor College of Medicine 0 1 0 1 0 0 0 1
NIHR Bioresource Rare Diseases, University of Cambridge 0 0 0 1 0 0 0 1
Undiagnosed Diseases Network, NIH 0 3 0 1 0 0 0 1
SIB Swiss Institute of Bioinformatics 0 0 0 0 0 0 1 1
Geisinger Autism and Developmental Medicine Institute, Geisinger Health System 0 0 0 0 0 0 1 1
Kariminejad - Najmabadi Pathology & Genetics Center 0 1 0 1 0 0 0 1
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen 0 6 0 1 0 0 0 1
Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Peking Union Medical College Hospital 0 0 0 1 0 0 0 1
Genome Diagnostics Laboratory, Amsterdam University Medical Center 0 1 0 1 0 0 0 1
Laboratory of Medical Genetics, University of Torino 0 1 0 1 0 0 0 1
Institute of Human Genetics, Heidelberg University 0 0 0 1 0 0 0 1
Biochemistry Laboratory of CDMU, Chengde Medical University 0 0 0 1 0 0 0 1
Reproductive Health Research and Development, BGI Genomics 0 0 0 1 0 0 0 1
Zotz-Klimas Genetics Lab, MVZ Zotz Klimas 0 1 0 1 0 0 0 1
Clinical Genomics Program, Stanford Medicine 0 0 0 1 0 0 0 1
Institute of Human Genetics, University Hospital Muenster 0 1 0 1 0 0 0 1
Genome-Nilou Lab 0 3 0 1 0 0 0 1
GenomeConnect - Simons Searchlight 0 1 0 1 0 0 0 1
Genetics Laboratory, UDIAT-Centre Diagnòstic, Hospital Universitari Parc Tauli 0 4 0 1 0 0 0 1
Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center 0 2 0 0 0 0 1 1
Neuberg Centre For Genomic Medicine, NCGM 0 1 0 1 0 0 0 1
Human Genetics Bochum, Ruhr University Bochum 0 0 0 1 0 0 0 1
Provincial Medical Genetics Program of British Columbia, University of British Columbia 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: 46
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_000275.3(OCA2):c.1327G>A (p.Val443Ile) rs121918166 0.00350
NM_024570.4(RNASEH2B):c.529G>A (p.Ala177Thr) rs75184679 0.00141
NM_152564.5(VPS13B):c.1248G>T (p.Gln416His) rs143024324 0.00111
NM_000275.3(OCA2):c.2339G>A (p.Gly780Asp) rs141949212 0.00021
NM_004004.6(GJB2):c.617A>G (p.Asn206Ser) rs111033294 0.00016
NM_017909.4(RMND1):c.713A>G (p.Asn238Ser) rs144972972 0.00013
NM_000275.3(OCA2):c.2359G>A (p.Ala787Thr) rs142988897 0.00006
NM_001673.5(ASNS):c.146G>A (p.Arg49Gln) rs769236847 0.00004
NM_000275.3(OCA2):c.1349C>T (p.Thr450Met) rs772019064 0.00003
NM_001543.5(NDST1):c.1831G>A (p.Gly611Ser) rs606231459 0.00001
NM_016529.6(ATP8A2):c.1756C>T (p.Arg586Ter) rs755133567 0.00001
NM_000282.4(PCCA):c.2040G>A (p.Ala680=) rs369982920
NM_000466.3(PEX1):c.2097dup (p.Ile700fs) rs61750415
NM_000489.6(ATRX):c.736C>T (p.Arg246Cys) rs122445105
NM_001029896.2(WDR45):c.827+2dup rs1602537729
NM_001080517.3(SETD5):c.2003C>G (p.Ser668Ter)
NM_001110792.2(MECP2):c.352C>T (p.Arg118Trp) rs28934907
NM_001110792.2(MECP2):c.961C>T (p.Arg321Trp) rs61751444
NM_001127222.2(CACNA1A):c.653C>T (p.Ser218Leu) rs121908225
NM_001164760.2(PRKAR1B):c.1003C>T (p.Arg335Trp) rs1475000361
NM_001197104.2(KMT2A):c.4171C>T (p.Gln1391Ter) rs2134311608
NM_001366145.2(TRPM3):c.3004G>A (p.Val1002Met) rs1564493599
NM_001370100.5(ZMYND11):c.1798C>T (p.Arg600Trp) rs797044854
NM_001371928.1(AHDC1):c.1122dup (p.Gly375fs) rs749294057
NM_001375380.1(EBF3):c.626G>A (p.Arg209Gln) rs1131692261
NM_001673.5(ASNS):c.736C>T (p.Arg246Cys) rs757828751
NM_001830.4(CLCN4):c.265G>A (p.Asp89Asn) rs1064794385
NM_001923.5(DDB1):c.637G>A (p.Glu213Lys) rs2134934938
NM_003907.3(EIF2B5):c.468C>G (p.Ile156Met)
NM_004859.4(CLTC):c.2325_2327del (p.Ile776del) rs1598233581
NM_005324.5(H3-3B):c.377A>G (p.Gln126Arg) rs2143629984
NM_005859.5(PURA):c.98del (p.Gly33fs)
NM_006218.4(PIK3CA):c.344G>T (p.Arg115Leu)
NM_006245.4(PPP2R5D):c.592G>A (p.Glu198Lys)
NM_006245.4(PPP2R5D):c.598G>A (p.Glu200Lys) rs863225079
NM_006852.6(TLK2):c.1015C>T (p.Arg339Trp) rs1567948262
NM_007118.4(TRIO):c.3232C>T (p.Arg1078Trp)
NM_012199.5(AGO1):c.1073A>G (p.Gln358Arg)
NM_012199.5(AGO1):c.536TCT[1] (p.Phe180del) rs1553154062
NM_012388.4(BLOC1S6):c.200C>G (p.Ser67Ter) rs772475341
NM_013328.4(PYCR2):c.647T>G (p.Met216Arg)
NM_016955.4(SEPSECS):c.114+3A>G
NM_016955.5(SEPSECS):c.808dup rs776969714
NM_018026.4(PACS1):c.607C>T (p.Arg203Trp) rs398123009
NM_025099.6(CTC1):c.833G>T (p.Gly278Val) rs768853291
NM_033310.3(KCNK4):c.515C>A (p.Ala172Glu) rs1565369746

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