ClinVar Miner

Submissions for variant NM_000368.4(TSC1):c.2209-3T>C (rs368309229)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Clinical Services Laboratory,Illumina RCV000467930 SCV000478209 uncertain significance Tuberous sclerosis 1 2018-01-12 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, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
Illumina Clinical Services Laboratory,Illumina RCV000357586 SCV000478210 likely benign Focal cortical dysplasia type II 2018-01-12 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.
Invitae RCV000467930 SCV000552330 benign Tuberous sclerosis 1 2019-12-31 criteria provided, single submitter clinical testing
GeneDx RCV000610023 SCV000732285 likely benign not specified 2018-02-09 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.
Ambry Genetics RCV001014788 SCV001175544 uncertain significance Hereditary cancer-predisposing syndrome 2018-12-12 criteria provided, single submitter clinical testing The c.2209-3T>C intronic variant results from a T to C substitution 3 nucleotides upstream from coding exon 16 in the TSC1 gene. This alteration is predicted to slightly decrease the efficiency of the native splice acceptor site by the BDGP in silico model and is not predicted to have a deleterious effect on splicing by the ESEfinder tool; however experimental evidence is not currently available. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

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