ClinVar Miner

Variants from Medical Molecular Genetics Department, National Research Center with conflicting interpretations

Location: Egypt  Primary collection method: clinical testing
Minimum review status of the submission from Medical Molecular Genetics Department, National Research Center: Collection method of the submission from Medical Molecular Genetics Department, National Research Center:
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
86 21 0 9 2 0 4 15

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
Medical Molecular Genetics Department, National Research Center pathogenic likely pathogenic uncertain significance benign
pathogenic 0 6 3 0
likely pathogenic 3 0 1 0
uncertain significance 0 0 0 1
benign 0 0 1 0

Submitter to submitter summary #

Total submitters: 12
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
Invitae 0 10 0 2 0 0 1 3
Laboratory of Diagnosis and Therapy of Lysosomal Disorders, University of Padova 0 1 0 2 0 0 1 3
Illumina Laboratory Services, Illumina 0 6 0 0 2 0 0 2
MGZ Medical Genetics Center 0 0 0 0 0 0 1 1
Counsyl 0 3 0 1 0 0 0 1
Bioscientia Institut fuer Medizinische Diagnostik GmbH, Sonic Healthcare 0 0 0 0 0 0 1 1
SIB Swiss Institute of Bioinformatics 0 0 0 1 0 0 0 1
Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard 0 0 0 1 0 0 0 1
Amsterdam Leukodystrophy Center, Amsterdam UMC 0 0 0 1 0 0 0 1
3billion 0 5 0 1 0 0 0 1
Institute of Human Genetics, Clinical Exome/Genome Diagnostics Group, University Hospital Bonn 0 0 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

All variants with conflicting interpretations #

Total variants: 15
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_021939.4(FKBP10):c.590A>G (p.Lys197Arg) rs34764749 0.06739
NM_000487.6(ARSA):c.346C>T (p.Arg116Ter) rs761860059 0.00002
NM_000046.5(ARSB):c.245T>G (p.Leu82Arg) rs749465732
NM_000046.5(ARSB):c.288C>G (p.Ser96Arg) rs1554032095
NM_000046.5(ARSB):c.479G>A (p.Arg160Gln) rs1196325597
NM_000152.5(GAA):c.1431del (p.Ile477fs) rs1598580364
NM_000487.6(ARSA):c.371G>A (p.Gly124Asp) rs2082689435
NM_001042492.3(NF1):c.2521A>C (p.Thr841Pro) rs2067066952
NM_001110792.2(MECP2):c.1193_1233del (p.Leu398fs) rs267608327
NM_001371623.1(TCOF1):c.4369_4372del (p.Glu1457fs)
NM_001399.5(EDA):c.620G>A (p.Gly207Glu) rs2020139491
NM_004183.4(BEST1):c.424_426dup (p.Ser142dup) rs1591284563
NM_020919.4(ALS2):c.1054_1061del (p.Leu352fs) rs1574786170
NM_020919.4(ALS2):c.4832G>A (p.Arg1611Gln) rs1689578912
NM_021939.4(FKBP10):c.21C>T (p.Pro7=) rs781985978

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