ClinVar Miner

Variants from Laboratory of Molecular Genetics (Pr. Bezieau's lab), CHU de Nantes with conflicting interpretations

Location: France  Primary collection method: clinical testing
Minimum review status of the submission from Laboratory of Molecular Genetics (Pr. Bezieau's lab), CHU de Nantes: Collection method of the submission from Laboratory of Molecular Genetics (Pr. Bezieau's lab), CHU de Nantes:
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
726 55 0 34 1 1 20 53

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
Laboratory of Molecular Genetics (Pr. Bezieau's lab), CHU de Nantes pathogenic likely pathogenic uncertain significance likely benign drug response
pathogenic 0 23 7 0 1
likely pathogenic 11 0 9 0 0
uncertain significance 3 2 0 1 0

Submitter to submitter summary #

Total submitters: 28
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 54 0 10 1 0 6 17
Invitae 0 17 0 4 1 0 6 11
CeGaT Center for Human Genetics Tuebingen 0 30 0 4 1 0 3 8
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 0 2 0 0 0 0 3 3
Baylor Genetics 0 0 0 2 0 0 0 2
Athena Diagnostics Inc 0 5 0 0 0 0 2 2
Molecular Diagnostics Lab, Nemours Children's Health, Delaware 0 1 0 2 0 0 0 2
Revvity Omics, Revvity 0 6 0 1 0 0 1 2
PreventionGenetics, part of Exact Sciences 0 9 0 1 1 0 0 2
Clinical Genetics and Genomics, Karolinska University Hospital 0 2 0 2 0 0 0 2
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ 0 9 0 2 0 0 0 2
Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein 0 1 0 1 0 0 1 2
Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center 0 3 0 0 0 0 1 1
Genome Diagnostics Laboratory, University Medical Center Utrecht 0 5 0 1 0 0 0 1
Eurofins Ntd Llc (ga) 0 10 0 1 0 0 0 1
PharmGKB 0 0 0 0 0 1 0 1
RettBASE 0 1 0 1 0 0 0 1
University of Washington Center for Mendelian Genomics, University of Washington 0 0 0 1 0 0 0 1
NeuroMeGen, Hospital Clinico Santiago de Compostela 0 0 0 1 0 0 0 1
Equipe Genetique des Anomalies du Developpement, Université de Bourgogne 0 0 0 1 0 0 0 1
Laboratoire de Génétique Moléculaire, CHU Bordeaux 0 1 0 1 0 0 0 1
Center for Personalized Medicine, Children's Hospital Los Angeles 0 1 0 1 0 0 0 1
Department of Genetics, Rouen University Hospital, Normandy Center for Genomic and Personalized Medicine 0 1 0 0 0 0 1 1
Institute for Human Genetics, University Hospital Essen 0 0 0 1 0 0 0 1
Molecular Genetics laboratory, Necker Hospital 0 1 0 1 0 0 0 1
AiLife Diagnostics, AiLife Diagnostics 0 2 0 1 0 0 0 1
Genetics Laboratory, UDIAT-Centre Diagnòstic, Hospital Universitari Parc Tauli 0 5 0 1 0 0 0 1
ClinGen Malignant Hyperthermia Susceptibility Variant Curation Expert Panel, ClinGen 0 0 0 0 0 0 1 1

All variants with conflicting interpretations #

Total variants: 53
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_016343.4(CENPF):c.3811A>G (p.Lys1271Glu) rs62000407 0.00238
NM_024570.4(RNASEH2B):c.529G>A (p.Ala177Thr) rs75184679 0.00141
NM_024678.6(NARS2):c.151C>T (p.Arg51Cys) rs367584549 0.00002
NM_000288.4(PEX7):c.854A>G (p.His285Arg) rs62653611 0.00001
NM_000391.4(TPP1):c.1593dup (p.Glu532fs) rs1216139602 0.00001
NM_001605.3(AARS1):c.259G>A (p.Asp87Asn) rs763757370 0.00001
NM_004380.3(CREBBP):c.5356C>T (p.Arg1786Cys) rs1555471394 0.00001
NM_033629.6(TREX1):c.218C>T (p.Pro73Leu) rs755919767 0.00001
NM_000156.6(GAMT):c.268G>A (p.Glu90Lys) rs1569006974
NM_000287.4(PEX6):c.2406del (p.Phe802fs) rs1554126965
NM_000287.4(PEX6):c.659G>T (p.Gly220Val) rs267608203
NM_000540.3(RYR1):c.14582G>A (p.Arg4861His) rs63749869
NM_000834.5(GRIN2B):c.2539C>T (p.Arg847Ter) rs879253931
NM_001032221.6(STXBP1):c.1168A>G (p.Ile390Val) rs1554778420
NM_001042681.2(RERE):c.3249dup (p.Ser1084fs) rs745806637
NM_001042681.2(RERE):c.4305C>G (p.His1435Gln) rs751232315
NM_001069.3(TUBB2A):c.1172G>A (p.Arg391His) rs1057521250
NM_001069.3(TUBB2A):c.728C>T (p.Pro243Leu) rs1554122947
NM_001080517.3(SETD5):c.2644C>T (p.Arg882Ter) rs1553635637
NM_001099922.3(ALG13):c.320A>G (p.Asn107Ser) rs398122394
NM_001110792.2(MECP2):c.455C>T (p.Ala152Val) rs28934908
NM_001110792.2(MECP2):c.953G>A (p.Arg318His) rs61751443
NM_001111125.3(IQSEC2):c.2911C>T (p.Arg971Ter) rs1131691887
NM_001161352.2(KCNMA1):c.1987A>G (p.Ile663Val) rs2092522027
NM_001170629.2(CHD8):c.3562C>T (p.Arg1188Ter) rs1555314911
NM_001256789.3(CACNA1F):c.2038C>T (p.Arg680Ter) rs782074040
NM_001282531.3(ADNP):c.2496_2499del (p.Asn832fs) rs587777523
NM_001321075.3(DLG4):c.925C>T (p.Arg309Ter) rs1182894684
NM_001371986.1(UNC80):c.5161C>T (p.Arg1721Cys) rs1266989763
NM_001372044.2(SHANK3):c.4874_4878dup (p.Pro1627fs) rs1603447373
NM_001374828.1(ARID1B):c.5763_5766del (p.Phe1921fs) rs1554237269
NM_001378615.1(CC2D2A):c.4465_4468del (p.Asp1489fs) rs797045437
NM_002074.5(GNB1):c.274G>A (p.Ala92Thr) rs1557889974
NM_003073.5(SMARCB1):c.1120C>T (p.Arg374Trp) rs1568963596
NM_003590.5(CUL3):c.1549_1552del (p.Ser517fs) rs1692335353
NM_003590.5(CUL3):c.493_494del (p.Leu165fs) rs1553523940
NM_003718.5(CDK13):c.2525A>G (p.Asn842Ser) rs878853160
NM_004187.5(KDM5C):c.1243-2A>G rs1569274606
NM_004333.6(BRAF):c.1574T>C (p.Leu525Pro) rs869025340
NM_004380.3(CREBBP):c.5603G>A (p.Arg1868Gln) rs1567263168
NM_005027.4(PIK3R2):c.1694C>G (p.Pro565Arg) rs1131691683
NM_005629.4(SLC6A8):c.945_949del (p.Phe315fs) rs1603216806
NM_013275.6(ANKRD11):c.1381_1384del (p.Glu461fs) rs1597464953
NM_014225.6(PPP2R1A):c.655T>C (p.Ser219Pro) rs2089686081
NM_015021.3(ZNF292):c.6160_6161del (p.Glu2054fs) rs1301328139
NM_016628.5(WAC):c.381+4_381+7del rs1564400647
NM_017946.4(FKBP14):c.362dup (p.Glu122fs) rs542489955
NM_021008.4(DEAF1):c.646A>G (p.Lys216Glu) rs1590017652
NM_021008.4(DEAF1):c.661T>C (p.Ser221Pro) rs1860668289
NM_031407.7(HUWE1):c.12037C>T (p.Arg4013Trp) rs121918525
NM_173630.4(RTTN):c.4295G>A (p.Arg1432His) rs1465962355
NM_177559.3(CSNK2A1):c.149A>G (p.Tyr50Cys) rs869312849
NM_177559.3(CSNK2A1):c.593A>G (p.Lys198Arg) rs869312840

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