ClinVar Miner

Submissions for variant NM_001754.5(RUNX1):c.486G>C (p.Arg162Ser)

dbSNP: rs1057519749
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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 RCV001290696 SCV001478833 likely pathogenic Hereditary thrombocytopenia and hematologic cancer predisposition syndrome 2024-06-24 reviewed by expert panel curation NM_001754.5(RUNX1):c.486G>C (p.Arg162Ser) is a missense variant which affects at least one of the following hotspot residues within the RHD: R107, K110, A134, R162, R166, S167, R169, G170, K194, T196, D198, R201, R204 (PM1). This variant is a missense change at the same residue (p.Arg162) where a different missense change has been previously established as a likely pathogenic variant (ClinVar ID 376022, 376021) based on MM-VCEP rules for RUNX1 (PM5_Supporting). The c.486G>C variant is the same amino acid change (p.Arg162Ser) as a previously established likely pathogenic variant (ClinVar ID 376019) curated using MM-VCEP rules for RUNX1 (PS1_Moderate). REVEL score=0.818, which is >0.75 threshold. SSF and MES show loss of a putative cryptic donor splice site at c.485 (PP3). This variant is completely absent from all population databases with at least 20x coverage for RUNX1 (PM2_Supporting). In summary, this variant meets criteria to be classified as likely pathogenic. ACMG/AMP criteria applied, as specified by the Myeloid Malignancy Variant Curation Expert Panel for RUNX1: PM1, PM5_supporting, PS1_moderate, PM2_supporting, PP3.
Database of Curated Mutations (DoCM) RCV000441948 SCV000504773 likely pathogenic Acute myeloid leukemia 2014-10-02 no assertion criteria provided literature only

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