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
370 71 0 34 1 0 12 45

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 benign
pathogenic 0 27 5 0
likely pathogenic 7 0 4 0
uncertain significance 1 1 0 1
likely benign 1 1 0 0

Submitter to submitter summary #

Total submitters: 34
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
Genetic Services Laboratory, University of Chicago 0 7 0 4 0 0 1 5
Institute of Human Genetics, University of Leipzig Medical Center 0 12 0 4 0 0 1 5
Invitae 0 35 0 1 1 0 2 4
Baylor Genetics 0 10 0 2 0 0 1 3
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics 0 3 0 1 0 0 2 3
Equipe Genetique des Anomalies du Developpement, Université de Bourgogne 0 3 0 3 0 0 0 3
SIB Swiss Institute of Bioinformatics 0 2 0 2 0 0 1 3
OMIM 0 31 0 1 0 0 1 2
Athena Diagnostics Inc 0 1 0 1 0 0 1 2
Blueprint Genetics 0 1 0 2 0 0 0 2
CeGaT Praxis fuer Humangenetik Tuebingen 0 9 0 0 0 0 2 2
Clinical Genetics laboratory, University of Goettingen 0 0 0 1 0 0 0 1
GeneDx 0 20 0 1 0 0 0 1
Molecular Diagnostics Lab,Nemours Alfred I. duPont Hospital for Children 0 0 0 1 0 0 0 1
Mendelics 0 2 0 1 0 0 0 1
GeneReviews 0 12 0 1 0 0 0 1
ClinVar Staff, National Center for Biotechnology Information (NCBI) 0 0 0 1 0 0 0 1
Illumina Clinical Services Laboratory,Illumina 0 3 0 0 0 0 1 1
UCLA Clinical Genomics Center, UCLA 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
Knight Diagnostic Laboratories, Oregon Health and Sciences University 0 0 0 1 0 0 0 1
Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics 0 0 0 0 0 0 1 1
NeuroMeGen,Hospital Clinico Santiago de Compostela 0 1 0 1 0 0 0 1
Diagnostics Division,Centre for DNA Fingerprinting and Diagnostics 0 0 0 1 0 0 0 1
Diagnostic Laboratory, Strasbourg University Hospital 0 1 0 0 0 0 1 1
Centre for Mendelian Genomics,University Medical Centre Ljubljana 0 3 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
The Molecular Genetic Diagnosis Center, Children’s Hospital of Fudan University 0 0 0 1 0 0 0 1
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen 0 3 0 1 0 0 0 1
Laboratoire de Genetique Moleculaire,Centre Hospitalier Universitaire de Bordeaux 0 0 0 1 0 0 0 1
Laboratory of Medical Genetics, National & Kapodistrian University of Athens 0 1 0 1 0 0 0 1
Department of Genetics, Rouen University Hospital, Normandy Center for Genomic and Personalized Medicine 0 1 0 1 0 0 0 1
Institute for Human Genetics, University Hospital Essen 0 0 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 45
Download table as spreadsheet
HGVS dbSNP
NM_000334.4(SCN4A):c.3466G>A (p.Ala1156Thr) rs80338958
NM_001029896.2(WDR45):c.397C>T (p.Arg133Ter) rs797046101
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_001110792.2(MECP2):c.1250C>T (p.Pro417Leu) rs61753016
NM_001110792.2(MECP2):c.509C>T (p.Thr170Met) rs28934906
NM_001110792.2(MECP2):c.535C>T (p.Arg179Trp) rs61748420
NM_001165963.4(SCN1A):c.4324G>T (p.Val1442Phe)
NM_001172509.2(SATB2):c.597+1G>A rs1559016679
NM_001184880.2(PCDH19):c.462C>G (p.Tyr154Ter) rs1569315876
NM_001193416.3(DDX3X):c.1595C>T (p.Thr532Met) rs1064795387
NM_001323289.2(CDKL5):c.1675C>T (p.Arg559Ter) rs267608395
NM_001330260.2(SCN8A):c.2549G>A (p.Arg850Gln)
NM_001352027.3(PHF21A):c.1741C>T (p.Arg581Ter)
NM_001366145.2(TRPM3):c.3004G>A (p.Val1002Met) rs1564493599
NM_001904.4(CTNNB1):c.1759C>T (p.Arg587Ter) rs1064796453
NM_001958.4(EEF1A2):c.364G>A (p.Glu122Lys)
NM_002074.5(GNB1):c.239T>C (p.Ile80Thr) rs752746786
NM_003748.4(ALDH4A1):c.1571G>A (p.Arg524Gln)
NM_004519.4(KCNQ3):c.689G>A (p.Arg230His)
NM_004975.4(KCNB1):c.934C>T (p.Arg312Cys)
NM_005055.5(RAPSN):c.848T>C (p.Leu283Pro) rs104894293
NM_006567.5(FARS2):c.667C>T (p.Arg223Cys) rs202060864
NM_006920.6(SCN1A):c.602+1G>A
NM_006940.6(SOX5):c.1711C>T (p.Arg571Trp) rs1565669640
NM_012123.4(MTO1):c.1282G>A (p.Ala428Thr) rs143747297
NM_012479.4(YWHAG):c.394C>T (p.Arg132Cys) rs1554616628
NM_014225.6(PPP2R1A):c.656C>T (p.Ser219Leu) rs1555791268
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_020732.3(ARID1B):c.2077G>T (p.Glu693Ter) rs1554294593
NM_020822.3(KCNT1):c.1421G>A (p.Arg474His)
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_024570.4(RNASEH2B):c.529G>A (p.Ala177Thr) rs75184679
NM_024757.5(EHMT1):c.3589C>T (p.Arg1197Trp)
NM_145239.3(PRRT2):c.649dup (p.Arg217fs)
NM_172107.4(KCNQ2):c.638G>A (p.Arg213Gln)

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