ClinVar Miner

Submissions for variant NM_138361.5(LRSAM1):c.1504-5C>G (rs377190920)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Clinical Services Laboratory,Illumina RCV000535609 SCV000477224 likely benign Charcot-Marie-Tooth disease type 2P 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 RCV000535609 SCV000652020 uncertain significance Charcot-Marie-Tooth disease type 2P 2017-06-07 criteria provided, single submitter clinical testing This sequence change falls in intron 19 of the LRSAM1 gene. It does not directly change the encoded amino acid sequence of the LRSAM1 protein. This variant is present in population databases (rs377190920, ExAC 0.02%). This variant has not been reported in the literature in individuals with an LRSAM1-related disease. ClinVar contains an entry for this variant (Variation ID: 365029). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site, but this prediction has not been confirmed by published transcriptional studies. In summary, this variant has uncertain impact on LRSAM1 function. The available evidence is currently insufficient to determine its role in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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