ClinVar Miner

Submissions for variant NM_001037.5(SCN1B):c.300C>T (p.Asp100=)

gnomAD frequency: 0.00539  dbSNP: rs16969927
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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000127900 SCV000171486 benign not specified 2013-03-15 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.
Eurofins Ntd Llc (ga) RCV000127900 SCV000228931 benign not specified 2014-08-28 criteria provided, single submitter clinical testing
Invitae RCV000197992 SCV000252898 benign Brugada syndrome 5 2024-02-01 criteria provided, single submitter clinical testing
Ambry Genetics RCV000617553 SCV000737804 benign Cardiovascular phenotype 2016-05-09 criteria provided, single submitter clinical testing Lines of evidence used in support of classification: General population or subpopulation frequency is too high to be a pathogenic mutation based on disease/syndrome prevalence and penetrance
Ambry Genetics RCV000716192 SCV000847029 benign Seizure 2016-05-09 criteria provided, single submitter clinical testing General population or subpopulation frequency is too high to be a pathogenic mutation based on disease/syndrome prevalence and penetrance
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000127900 SCV000918185 benign not specified 2017-10-23 criteria provided, single submitter clinical testing Variant summary: The SCN1B c.300C>T (p.Asp100Asp) variant involves the alteration of a conserved nucleotide causing a synonymous change and 5/5 splice prediction tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. This variant was found in 456/277158 (5 homozygotes) control chromosomes (gnomAD) at a frequency of 0.0016453, which is approximately 165 times the estimated maximal expected allele frequency of a pathogenic SCN1B variant (0.00001), suggesting this variant is likely a benign polymorphism. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as benign. The variant of interest has not, to our knowledge, been reported in affected individuals via publications and/or reputable databases/clinical diagnostic laboratories; nor evaluated for functional impact by in vivo/vitro studies. Taken together, this variant is classified as benign.
Illumina Laboratory Services, Illumina RCV000197992 SCV001281961 benign Brugada syndrome 5 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 Laboratory Services, Illumina RCV001123152 SCV001281962 likely benign Generalized epilepsy with febrile seizures plus, type 1 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.
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV001812111 SCV002048056 benign not provided 2021-04-13 criteria provided, single submitter clinical testing

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