ClinVar Miner

Variants from Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit, IRCCS Fondazione Stella Maris with conflicting interpretations

Location: Italy  Primary collection method: research
Minimum review status of the submission from Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit, IRCCS Fondazione Stella Maris: Collection method of the submission from Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit, IRCCS Fondazione Stella Maris:
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
182 33 0 16 0 0 10 25

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
Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit, IRCCS Fondazione Stella Maris pathogenic likely pathogenic uncertain significance likely benign
pathogenic 0 14 3 0
likely pathogenic 2 0 7 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 14 0 0 0 0 4 4
Revvity Omics, Revvity 0 3 0 2 0 0 1 3
3billion 0 6 0 2 0 0 1 3
Genomics England Pilot Project, Genomics England 0 1 0 3 0 0 0 3
OMIM 0 20 0 2 0 0 0 2
Baylor Genetics 0 8 0 0 0 0 2 2
MGZ Medical Genetics Center 0 6 0 1 0 0 1 2
Counsyl 0 1 0 1 0 0 1 2
Natera, Inc. 0 3 0 0 0 0 2 2
Fulgent Genetics, Fulgent Genetics 0 5 0 2 0 0 0 2
Institute of Human Genetics, University of Leipzig Medical Center 0 7 0 2 0 0 0 2
SIB Swiss Institute of Bioinformatics 0 1 0 2 0 0 0 2
Genome-Nilou Lab 0 4 0 0 0 0 2 2
Genetic Services Laboratory, University of Chicago 0 4 0 1 0 0 0 1
Institute of Medical Molecular Genetics, University of Zurich 0 0 0 1 0 0 0 1
Mendelics 0 5 0 0 0 0 1 1
Genomic Research Center, Shahid Beheshti University of Medical Sciences 0 3 0 0 0 0 1 1
Centre for Mendelian Genomics, University Medical Centre Ljubljana 0 0 0 1 0 0 0 1
Equipe Genetique des Anomalies du Developpement, Université de Bourgogne 0 0 0 1 0 0 0 1
Tartaglia Lab, Genetics and Rare Diseases Research Division, Bambino Gesu' Children's Hospital 0 0 0 1 0 0 0 1
Consultorio y Laboratorio de Neurogenética, Hospital JM Ramos Mejia 0 0 0 0 0 0 1 1
Johns Hopkins Genomics, Johns Hopkins University 0 0 0 1 0 0 0 1
Myriad Genetics, Inc. 0 2 0 1 0 0 0 1
Pediatric Department, Xiangya Hospital, Central South University 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
DASA 0 3 0 1 0 0 0 1
Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein 0 3 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 25
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_003119.4(SPG7):c.1529C>T (p.Ala510Val) rs61755320 0.00361
NM_000303.3(PMM2):c.422G>A (p.Arg141His) rs28936415 0.00338
NM_007055.4(POLR3A):c.1909+22G>A rs191875469 0.00156
NM_005861.4(STUB1):c.433A>C (p.Lys145Gln) rs146251364 0.00063
NM_015506.3(MMACHC):c.472T>C (p.Phe158Leu) rs201312386 0.00019
NM_001378969.1(KCND3):c.1646G>A (p.Arg549His) rs35027371 0.00016
NM_014874.4(MFN2):c.1987C>T (p.Arg663Cys) rs369762154 0.00011
NM_000033.4(ABCD1):c.2087A>T (p.Lys696Met) rs782157913 0.00006
NM_000051.4(ATM):c.8147T>C (p.Val2716Ala) rs587782652 0.00004
NM_000303.3(PMM2):c.323C>T (p.Ala108Val) rs200503569 0.00001
NM_003119.4(SPG7):c.1972G>A (p.Ala658Thr) rs2058661391 0.00001
NM_005559.4(LAMA1):c.184C>T (p.Arg62Ter) rs758223206 0.00001
NM_020320.5(RARS2):c.517G>A (p.Asp173Asn) rs769045045 0.00001
NM_001114748.2(TMEM240):c.196G>A (p.Gly66Arg) rs1057518011
NM_001114748.2(TMEM240):c.509C>T (p.Pro170Leu) rs606231451
NM_001127222.2(CACNA1A):c.3310_3315dup (p.Gly1104_Pro1105dup) rs776584949
NM_001127222.2(CACNA1A):c.4466T>C (p.Phe1489Ser) rs121908233
NM_001127222.2(CACNA1A):c.4927G>A (p.Asp1643Asn) rs1064795531
NM_001195248.2(APTX):c.668T>C (p.Leu223Pro) rs267606665
NM_001244008.2(KIF1A):c.32G>A (p.Arg11Gln) rs1575654528
NM_001378452.1(ITPR1):c.722G>A (p.Arg241Lys) rs2125159664
NM_003119.4(SPG7):c.1231G>A (p.Asp411Asn) rs745444834
NM_004974.4(KCNA2):c.881G>A (p.Arg294His) rs886041761
NM_006946.4(SPTBN2):c.1438C>T (p.Arg480Trp) rs397514749
NM_130837.3(OPA1):c.2873_2876del rs80356530

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