ClinVar Miner

Submissions for variant NM_001754.5(RUNX1):c.1056C>T (p.Ala352=)

dbSNP: rs2145877419
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ClinGen Myeloid Malignancy Variant Curation Expert Panel RCV004595645 SCV005088378 likely benign Hereditary thrombocytopenia and hematologic cancer predisposition syndrome 2024-06-24 reviewed by expert panel curation NM_001754.5(RUNX1):c.1056C>T (p.Ala352=) is a synonymous variant. This variant is completely absent from all population databases with at least 20x coverage for RUNX1 in gnomAD v2.1.1 and v3.1.2 (PM2_supporting). SpliceAI predicts no impact to splicing (score: 0.00) (BP4). Evolutionary conservation prediction algorithms predict the site as not being conserved (PhyloP score 0.495 (BP7). This variant was reported in ClinVar in 2022 by Invitae but the affected status of the proband is unknown (Variation ID 1577145). In summary, this variant meets criteria to be classified as likely benign. ACMG/AMP criteria applied, as specified by the Myeloid Malignancy Variant Curation Expert Panel for RUNX1: PM2_supporting, BP4, BP7.
Labcorp Genetics (formerly Invitae), Labcorp RCV002087834 SCV002377960 likely benign Hereditary thrombocytopenia and hematological cancer predisposition syndrome associated with RUNX1 2022-07-06 criteria provided, single submitter clinical testing
GeneDx RCV004763329 SCV005370876 uncertain significance not provided 2024-04-07 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis indicates that this variant does not alter splicing; Has not been previously published as pathogenic or benign to our knowledge

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