ClinVar Miner

Submissions for variant NM_000344.3(SMN1):c.*3+1G>A (rs1290417835)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Molecular Diagnostics Lab,Nemours Alfred I. duPont Hospital for Children RCV000785817 SCV000924387 likely pathogenic not provided 2016-03-21 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV001174771 SCV001338093 likely pathogenic Spinal muscular atrophy 2020-01-20 criteria provided, single submitter clinical testing Variant summary: SMN1 c.*3+1G>A is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. Several computational tools predict a significant impact on normal splicing: Three predict the variant abolishes a 5' splicing donor site. However, these predictions have yet to be confirmed by functional studies. The variant was absent in 247916 control chromosomes. To our knowledge, no occurrence of c.*3+1G>A in individuals affected with Spinal Muscular Atrophy and no experimental evidence demonstrating its impact on protein function have been reported. However, c.*3+1G>C has been reported in patients with Spinal muscular atrophy (HGMD database). One clinical diagnostic laboratory has submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation and classified the variant as likely pathogenic. Based on the evidence outlined above, the variant was classified as likely pathogenic.

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