ClinVar Miner

Submissions for variant NM_001754.5(RUNX1):c.1162T>A (p.Ser388Thr)

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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 RCV004736323 SCV005367740 uncertain significance Hereditary thrombocytopenia and hematologic cancer predisposition syndrome 2024-09-25 reviewed by expert panel curation NM_001754.5(RUNX1):c.1162T>A (p.Ser388Thr) is a missense variant. This variant is completely absent from all population databases with at least 20x coverage for RUNX1 in gnomAD (PM2_supporting). This missense variant has a REVEL score <0.50 (0.154) and a spliceAI score <0.2 (0.0) (BP4). The c.1162T>A variant is the same amino acid change (p.Ser388Thr) as a previously established likely pathogenic variant (ClinVar ID 561222) curated using MM-VCEP rules for RUNX1 and RNA data or agreement in splicing predictors (SSF and MES) show no splicing effects (PS1_Moderate). In summary, the clinical significance of this variant is uncertain. ACMG/AMP criteria applied, as specified by the Myeloid Malignancy Variant Curation Expert Panel for RUNX1: PM2_supporting, BP4, PS1_moderate.
Ambry Genetics RCV003191652 SCV003877645 uncertain significance Inborn genetic diseases 2023-02-28 criteria provided, single submitter clinical testing The c.1162T>A (p.S388T) alteration is located in exon 9 (coding exon 8) of the RUNX1 gene. This alteration results from a T to A substitution at nucleotide position 1162, causing the serine (S) at amino acid position 388 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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