ClinVar Miner

Variants from Diagnostic Laboratory, Strasbourg University Hospital with conflicting interpretations

Location: France  Primary collection method: clinical testing
Minimum review status of the submission from Diagnostic Laboratory, Strasbourg University Hospital: Collection method of the submission from Diagnostic Laboratory, Strasbourg University Hospital:
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
681 32 0 13 3 0 12 26

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
Diagnostic Laboratory, Strasbourg University Hospital pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 0 7 3 0 0
likely pathogenic 6 0 5 0 0
uncertain significance 3 1 0 2 1
likely benign 0 0 1 0 0

Submitter to submitter summary #

Total submitters: 24
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 16 0 6 2 0 7 15
CeGaT Center for Human Genetics Tuebingen 0 9 0 4 2 0 0 6
Eurofins Ntd Llc (ga) 0 2 0 2 1 0 2 5
Genetic Services Laboratory, University of Chicago 0 0 0 0 1 0 3 4
PreventionGenetics, part of Exact Sciences 0 4 0 1 0 0 2 3
Invitae 0 6 0 0 1 0 2 3
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen 0 0 0 2 1 0 0 3
Athena Diagnostics Inc 0 0 0 0 1 0 1 2
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ 0 3 0 1 1 0 0 2
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine 0 0 0 0 0 0 1 1
Revvity Omics, Revvity 0 4 0 0 0 0 1 1
Genome Diagnostics Laboratory, University Medical Center Utrecht 0 0 0 0 1 0 0 1
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 0 1 0 0 0 0 1 1
Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics 0 0 0 0 1 0 0 1
Centre de Biologie Pathologie Génétique, Centre Hospitalier Universitaire de Lille 0 1 0 0 0 0 1 1
NIHR Bioresource Rare Diseases, University of Cambridge 0 0 0 1 0 0 0 1
SIB Swiss Institute of Bioinformatics 0 0 0 1 0 0 0 1
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) 0 0 0 0 1 0 0 1
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center 0 1 0 1 0 0 0 1
Génétique des Maladies du Développement, Hospices Civils de Lyon 0 1 0 0 0 0 1 1
Raymond Lab, University of Cambridge 0 0 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
Autoinflammatory diseases unit, CHU de Montpellier 0 0 0 1 0 0 0 1
Pediatric Genetics Clinic, Sheba Medical Center 0 0 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 26
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_001371986.1(UNC80):c.1806G>C (p.Gln602His) rs200473652 0.00163
NM_007254.4(PNKP):c.1029+2T>C rs199919568 0.00115
NM_007254.4(PNKP):c.1549C>T (p.Gln517Ter) rs774995635 0.00019
NM_005045.4(RELN):c.2015C>T (p.Pro672Leu) rs201044262 0.00016
NM_001083961.2(WDR62):c.1480G>A (p.Gly494Arg) rs587784543 0.00006
NM_001387263.1(PATL2):c.478C>T (p.Arg160Ter) rs548527219 0.00003
NM_001165963.4(SCN1A):c.2576G>A (p.Arg859His) rs398123588 0.00001
NM_001195553.2(DCX):c.587G>A (p.Arg196His) rs56030372 0.00001
NM_000489.6(ATRX):c.109C>T (p.Arg37Ter) rs122445108
NM_001032221.6(STXBP1):c.416C>T (p.Pro139Leu) rs796053353
NM_001040142.2(SCN2A):c.2654C>T (p.Thr885Ile) rs1699477928
NM_001069.3(TUBB2A):c.872A>C (p.Gln291Pro) rs863224939
NM_001077350.3(NPRL3):c.980C>T (p.Pro327Leu) rs1898841618
NM_001134407.3(GRIN2A):c.1007+1G>A rs397518465
NM_001144967.3(NEDD4L):c.1402C>T (p.Arg468Trp) rs1199827684
NM_001165963.4(SCN1A):c.1129C>T (p.Arg377Ter) rs794726799
NM_001195553.2(DCX):c.557G>A (p.Arg186His) rs587783563
NM_001271.4(CHD2):c.1934C>T (p.Thr645Met) rs2053619460
NM_001330260.2(SCN8A):c.5630A>G (p.Asn1877Ser) rs587780455
NM_001352027.3(PHF21A):c.1741C>T (p.Arg581Ter)
NM_003070.5(SMARCA2):c.3602C>T (p.Ala1201Val) rs281875189
NM_004519.4(KCNQ3):c.688C>T (p.Arg230Cys) rs796052676
NM_005249.5(FOXG1):c.460dup (p.Glu154fs) rs398124204
NM_006218.4(PIK3CA):c.2740G>A (p.Gly914Arg) rs587776932
NM_145239.3(PRRT2):c.647C>T (p.Pro216Leu) rs76335820
NM_172362.3(KCNH1):c.1070G>A (p.Arg357Gln) rs886041300

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