ClinVar Miner

Submissions for variant NM_001754.5(RUNX1):c.805+12723_805+12724del

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ClinGen Myeloid Malignancy Variant Curation Expert Panel RCV005001376 SCV005627325 likely benign Hereditary thrombocytopenia and hematologic cancer predisposition syndrome 2025-01-15 reviewed by expert panel curation NM_001754.5(RUNX1):c.805+12723_805+12724del is an intronic variant which is completely absent from all population databases with at least 20x coverage for RUNX1 (PM2_supporting). This variant has a SpliceAI score ≤ 0.20 (Δ score: 0.00) (BP4), and evolutionary conservation algorithms predict the site as not being conserved (PhyloP score ≤ 2.0 (0.17)) (BP7). 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.
PreventionGenetics, part of Exact Sciences RCV003391652 SCV004111007 uncertain significance RUNX1-related disorder 2023-07-03 criteria provided, single submitter clinical testing The RUNX1 c.734_735delCA variant is predicted to result in a frameshift and premature protein termination (p.Thr245Serfs*67). Using the canonical transcript (NM_001754), this variant is as referred to as c.805+12723_805+12724delCA, which is not predicted to impact splicing based on available splicing prediction programs (Alamut Visual Plus v1.6.1). To our knowledge, this variant has not been reported in the literature or in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. Although we suspect that this variant may be benign, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

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