ClinVar Miner

Variants from Laboratory of Medical Genetics, University of Torino with conflicting interpretations

Location: Italy  Primary collection method: research
Minimum review status of the submission from Laboratory of Medical Genetics, University of Torino: Collection method of the submission from Laboratory of Medical Genetics, University of Torino:
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
157 25 0 21 1 0 7 28

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 Medical Genetics, University of Torino pathogenic likely pathogenic uncertain significance benign
pathogenic 0 14 2 0
likely pathogenic 8 0 3 0
uncertain significance 0 2 0 1

Submitter to submitter summary #

Total submitters: 27
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 11 0 2 1 0 2 5
OMIM 0 12 0 3 0 0 0 3
Mendelics 0 2 0 2 0 0 0 2
Baylor Genetics 0 6 0 0 0 0 1 1
Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center 0 3 0 1 0 0 0 1
Center for Human Genetics, Inc, Center for Human Genetics, Inc 0 0 0 1 0 0 0 1
Molecular Diagnostics Lab, Nemours Children's Health, Delaware 0 0 0 1 0 0 0 1
Fulgent Genetics, Fulgent Genetics 0 3 0 1 0 0 0 1
ClinVar Staff, National Center for Biotechnology Information (NCBI) 0 0 0 1 0 0 0 1
NeuroMeGen, Hospital Clinico Santiago de Compostela 0 0 0 1 0 0 0 1
Centre for Mendelian Genomics, University Medical Centre Ljubljana 0 1 0 0 0 0 1 1
Genetics and Molecular Pathology, SA Pathology 0 1 0 1 0 0 0 1
Groupe Hospitalier Pitie Salpetriere, UF Genomique du Developpement, Assistance Publique Hopitaux de Paris 0 0 0 1 0 0 0 1
Institute of Human Genetics, University of Leipzig Medical Center 0 5 0 0 0 0 1 1
SIB Swiss Institute of Bioinformatics 0 0 0 0 0 0 1 1
Laboratoire de Génétique Moléculaire, CHU Bordeaux 0 1 0 1 0 0 0 1
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen 0 0 0 1 0 0 0 1
Laboratory of Medical Genetics, University of Torino 207 2 0 1 0 0 0 1
Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn 0 0 0 0 0 0 1 1
Genome-Nilou Lab 0 1 0 1 0 0 0 1
GenomeConnect - Simons Searchlight 0 1 0 1 0 0 0 1
3billion 0 5 0 1 0 0 0 1
Neuberg Centre For Genomic Medicine, NCGM 0 0 0 0 0 0 1 1
Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein 0 1 0 1 0 0 0 1
ClinGen Cerebral Creatine Deficiency Syndromes Variant Curation Expert Panel, ClinGen 0 0 0 1 0 0 0 1
Clinical Laboratory Sciences Program (CLSP), King Saud bin Abdulaziz University for Health Sciences (KSAU-HS) 0 1 0 1 0 0 0 1
St. Anna Children's Cancer Research Institute (CCRI) 0 0 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 28
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_177550.5(SLC13A5):c.655G>A (p.Gly219Arg) rs144332569 0.00009
NM_000202.8(IDS):c.1478G>A (p.Arg493His) rs782347729 0.00002
NM_015909.4(NBAS):c.1501C>T (p.Arg501Ter) rs759960319 0.00001
NM_001080517.3(SETD5):c.3855dup (p.Ser1286fs) rs1553641476
NM_001101.5(ACTB):c.589G>A (p.Gly197Ser) rs1554329317
NM_001110792.2(MECP2):c.953G>A (p.Arg318His) rs61751443
NM_001111125.3(IQSEC2):c.3365G>A (p.Arg1122His) rs868984872
NM_001372044.2(SHANK3):c.3952dup (p.Gln1318fs)
NM_001375524.1(TRRAP):c.5713A>G (p.Lys1905Glu) rs1791437854
NM_003073.5(SMARCB1):c.110G>A (p.Arg37His) rs398122368
NM_003482.4(KMT2D):c.4395dup (p.Lys1466fs) rs1555195118
NM_003491.4(NAA10):c.346C>T (p.Arg116Trp)
NM_005324.5(H3-3B):c.377A>G (p.Gln126Arg) rs2143629984
NM_005629.4(SLC6A8):c.1428C>G (p.Tyr476Ter)
NM_006852.6(TLK2):c.1586A>G (p.Asp529Gly) rs2082811958
NM_007327.4(GRIN1):c.421G>A (p.Val141Met) rs1293947350
NM_014023.4(WDR37):c.356C>T (p.Ser119Phe) rs1589088690
NM_014141.6(CNTNAP2):c.1777+2T>C
NM_014927.5(CNKSR2):c.1198C>T (p.Arg400Ter)
NM_017780.4(CHD7):c.3082A>G (p.Ile1028Val) rs121434338
NM_018026.4(PACS1):c.607C>T (p.Arg203Trp) rs398123009
NM_019597.5(HNRNPH2):c.617G>A (p.Arg206Gln) rs886039764
NM_020822.3(KCNT1):c.108del (p.Arg37fs)
NM_031844.3(HNRNPU):c.16delinsATT (p.Val6fs) rs1135401794
NM_031844.3(HNRNPU):c.2304_2305del (p.Gly769fs) rs794729648
NM_170675.5(MEIS2):c.992GAA[2] (p.Arg333del) rs879255264
NM_194454.3(KRIT1):c.1201_1204del (p.Gln401fs) rs1057517753
NM_205861.3(DHDDS):c.110G>A (p.Arg37His) rs1553121073

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