ClinVar Miner

Submissions for variant NM_182961.4(SYNE1):c.10037C>A (p.Ser3346Tyr) (rs150170988)

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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000179620 SCV000231894 benign not specified 2015-02-18 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000283926 SCV000461323 benign Emery-Dreifuss muscular dystrophy 4, autosomal dominant 2018-01-13 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
Illumina Clinical Services Laboratory,Illumina RCV000341509 SCV000461324 likely benign Spinocerebellar ataxia, autosomal recessive 8 2018-01-13 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.
CeGaT Praxis fuer Humangenetik Tuebingen RCV000415926 SCV000493376 likely benign not provided 2020-04-01 criteria provided, single submitter clinical testing
GeneDx RCV000179620 SCV000514835 benign not specified 2017-04-12 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Invitae RCV001084029 SCV000648998 likely benign Spinocerebellar ataxia, autosomal recessive 8; Emery-Dreifuss muscular dystrophy 4, autosomal dominant 2019-12-31 criteria provided, single submitter clinical testing
Athena Diagnostics Inc RCV000415926 SCV000844196 benign not provided 2017-09-21 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000415926 SCV000884636 likely benign not provided 2017-08-07 criteria provided, single submitter clinical testing The c.10058C>A; p.Ser3353Tyr variant (rs150170988), to our knowledge, is not reported in the medical literature, gene specific variation databases, nor has it been previously identified by our laboratory. This variant is listed in the genome Aggregation Database (gnomAD) with a non-Finnish European population frequency of 0.6% (identified on 775 out of 126,720 chromosomes, including 5 homozygotes) and is classified as benign/likely benign in ClinVar (variant ID: 198335). The serine at position 3353 is weakly conserved, considering 12 species, and computational analyses of the effects of the p.Ser3353Tyr variant on protein structure and function do not predict a deleterious effect (SIFT: tolerated, PolyPhen-2: benign). Based on the available information, the p.Ser3353Tyr variant is likely to be benign.

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