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 Variants with at least 2 submissions 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 kind of conflict
202 45 0 31 2 0 19 48

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 21 8 0
likely pathogenic 10 0 8 0
uncertain significance 2 2 0 2
likely benign 1 1 0 0

Submitter to submitter summary #

Total submitters: 27
Download table as spreadsheet
Submitter Variants with only 1 submission Variants with at least 2 submissions 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 kind of conflict
Invitae 0 33 0 2 2 0 6 10
Genetic Services Laboratory, University of Chicago 0 6 0 5 0 0 2 7
GeneDx 0 45 0 5 0 0 2 7
Ambry Genetics 0 13 0 4 0 0 3 7
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics 0 8 0 2 0 0 5 7
OMIM 0 24 0 3 0 0 2 5
Athena Diagnostics Inc 0 3 0 0 0 0 2 2
GeneReviews 0 10 0 1 0 0 1 2
NIHR Bioresource Rare Diseases, University of Cambridge 0 1 0 2 0 0 0 2
Baylor Genetics 0 8 0 0 0 0 1 1
Mendelics 0 2 0 1 0 0 0 1
ClinVar Staff, National Center for Biotechnology Information (NCBI) 0 0 0 1 0 0 0 1
UCLA Clinical Genomics Center, UCLA 0 1 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
Lupski Lab, Baylor-Hopkins CMG, Baylor College of Medicine 0 1 0 1 0 0 0 1
NeuroMeGen,Hospital Clinico Santiago de Compostela 0 1 0 1 0 0 0 1
Laboratory of Molecular Genetics,CHU RENNES 0 0 0 1 0 0 0 1
CeGaT Praxis fuer Humangenetik Tuebingen 0 2 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
SIB Swiss Institute of Bioinformatics 0 2 0 0 0 0 1 1
Geisinger Autism and Developmental Medicine Institute,Geisinger Health System 0 0 0 1 0 0 0 1
Laboratoire de Génétique Moléculaire Institut de Recherche Necker Enfants Malades,CHU Paris - Hôpital Necker-Enfants Malades 0 1 0 1 0 0 0 1
Génétique des Maladies du Développement, Hospices Civils de Lyon 290 4 0 0 0 0 1 1
Raymond Lab,University of Cambridge 0 0 0 1 0 0 0 1
Laboratory of Medical Genetics, National & Kapodistrian University of Athens 0 0 0 1 0 0 0 1
Department of Genetics, Rouen University Hospital, Normandy Center for Genomic and Personalized Medicine 0 0 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: 48
Download table as spreadsheet
HGVS dbSNP
NM_000334.4(SCN4A):c.3466G>A (p.Ala1156Thr) rs80338958
NM_000742.4(CHRNA2):c.937C>T (p.Leu313Phe) rs886042322
NM_000834.4(GRIN2B):c.2065G>A (p.Gly689Ser) rs869312868
NM_000834.4(GRIN2B):c.3028C>T (p.Pro1010Ser) rs956362869
NM_001029896.2(WDR45):c.397C>T (p.Arg133Ter) rs797046101
NM_001040142.2(SCN2A):c.1199C>G (p.Thr400Arg) rs776206684
NM_001040142.2(SCN2A):c.4886G>A (p.Arg1629His) rs796053157
NM_001040142.2(SCN2A):c.605C>T (p.Ala202Val) rs1553567409
NM_001101802.2(PHF21A):c.1738C>T (p.Arg580Ter) rs1565138763
NM_001110792.2(MECP2):c.1250C>T (p.Pro417Leu) rs61753016
NM_001110792.2(MECP2):c.535C>T (p.Arg179Trp) rs61748420
NM_001127221.1(CACNA1A):c.2137G>A (p.Ala713Thr) rs886037945
NM_001127644.2(GABRA1):c.335G>A (p.Arg112Gln) rs587777308
NM_001128849.2(SMARCA4):c.2936G>A (p.Arg979Gln) rs797045981
NM_001134407.3(GRIN2A):c.2146G>A (p.Ala716Thr) rs762659685
NM_001172509.2(SATB2):c.1165C>T (p.Arg389Cys) rs1057521083
NM_001172509.2(SATB2):c.597+1G>A rs1559016679
NM_001271.4(CHD2):c.2095C>T (p.Arg699Trp) rs1131691515
NM_001330260.2(SCN8A):c.2549G>A (p.Arg850Gln) rs587780586
NM_001330260.2(SCN8A):c.4877G>A (p.Arg1626His) rs886044328
NM_001958.4(EEF1A2):c.364G>A (p.Glu122Lys) rs786205866
NM_003482.3(KMT2D):c.15461G>A (p.Arg5154Gln) rs886043497
NM_003688.3(CASK):c.2129A>G (p.Asp710Gly) rs137852818
NM_004519.4(KCNQ3):c.689G>A (p.Arg230His) rs749205120
NM_004975.4(KCNB1):c.934C>T (p.Arg312Cys) rs886039396
NM_006245.4(PPP2R5D):c.592G>A (p.Glu198Lys) rs863225082
NM_006516.3(SLC2A1):c.988C>T (p.Arg330Ter) rs80359826
NM_006567.5(FARS2):c.667C>T (p.Arg223Cys) rs202060864
NM_006920.6(SCN1A):c.4880T>A (p.Ile1627Asn) rs1057521079
NM_006920.6(SCN1A):c.5033T>C (p.Met1678Thr) rs1559104676
NM_006920.6(SCN1A):c.602+1G>A rs794726827
NM_006940.6(SOX5):c.1711C>T (p.Arg571Trp) rs1565669640
NM_007118.4(TRIO):c.3232C>T (p.Arg1078Trp) rs1554065887
NM_007327.4(GRIN1):c.679G>C (p.Asp227His) rs869312865
NM_015267.4(CUX2):c.1768G>A (p.Glu590Lys) rs1565909334
NM_018026.4(PACS1):c.607C>T (p.Arg203Trp) rs398123009
NM_020822.3(KCNT1):c.1421G>A (p.Arg474His) rs397515404
NM_020822.3(KCNT1):c.2849G>A (p.Arg950Gln) rs886043455
NM_020822.3(KCNT1):c.2896G>A (p.Ala966Thr) rs1424788778
NM_020988.3(GNAO1):c.118G>C (p.Gly40Arg) rs886041715
NM_020988.3(GNAO1):c.680C>T (p.Ala227Val) rs797045599
NM_022455.4(NSD1):c.4378+1G>A rs587784115
NM_024757.5(EHMT1):c.3589C>T (p.Arg1197Trp) rs137852727
NM_144495.2(PQBP1):c.293-341AG[4] rs606231193
NM_145239.3(PRRT2):c.649dup (p.Arg217fs) rs587778771
NM_152296.5(ATP1A3):c.2401G>A (p.Asp801Asn) rs80356537
NM_172107.4(KCNQ2):c.430C>T (p.Arg144Trp) rs1555873985
NM_172107.4(KCNQ2):c.638G>A (p.Arg213Gln) rs397514581

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