ClinVar Miner

Submissions for variant NM_017654.4(SAMD9):c.1058C>T (p.Thr353Met)

gnomAD frequency: 0.00034  dbSNP: rs138478808
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Johns Hopkins Genomics, Johns Hopkins University RCV001260988 SCV001438363 likely benign MIRAGE syndrome 2020-10-02 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001363225 SCV001559327 likely benign not provided 2025-01-23 criteria provided, single submitter clinical testing
St. Jude Molecular Pathology, St. Jude Children's Research Hospital RCV001260988 SCV002584775 uncertain significance MIRAGE syndrome 2022-08-01 criteria provided, single submitter clinical testing The SAMD9 c.1058C>T (p.Thr353Met) missense change has a maximum subpopulation frequency of 0.079% in gnomAD v2.1.1 (https://gnomad.broadinstitute.org/). The in silico tool REVEL predicts a benign effect of this variant on protein function, however in silico predictions have not been found to correlate with syndromic risk for SAMD9 variants and are thus not considered supporting evidence of a pathogenic or benign effect (PMID: 34621053). To our knowledge, this variant has not been reported in individuals with SAMD9-associated conditions. In summary, the evidence currently available is insufficient to determine the clinical significance of this variant. It has therefore been classified as of uncertain significance.
PreventionGenetics, part of Exact Sciences RCV004738222 SCV005345755 likely benign SAMD9-related disorder 2024-04-17 no assertion criteria provided clinical testing This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).

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