ClinVar Miner

Submissions for variant NM_001754.5(RUNX1):c.1257G>A (p.Val419=)

gnomAD frequency: 0.00003  dbSNP: rs1172332120
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ClinGen Myeloid Malignancy Variant Curation Expert Panel RCV004999550 SCV000965647 likely benign Hereditary thrombocytopenia and hematologic cancer predisposition syndrome 2025-01-15 reviewed by expert panel curation NM_001754.5(RUNX1):c.1257G>A (p.Val419=) is a synonymous variant which meets criteria for likely benign classification. The MAF is 0.0001369 (0.01369%, 7/51146 alleles) in the Admixed American subpopulation of the gnomAD v4.1.0 cohort, which is between 0.00015 (0.015%) and 0.0015 (0.15%) (BS1). It has a SpliceAI score ≤ 0.20 (Donor gain Δ score 0.01) (BP4), and evolutionary conservation algorithms predict the site as not being conserved (PhyloP score ≤ 2.0 (0.370)) (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: BS1, BP4, BP7.
Genetic Services Laboratory, University of Chicago RCV000501631 SCV000596875 uncertain significance not specified 2016-09-28 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000533622 SCV000638124 likely benign Hereditary thrombocytopenia and hematological cancer predisposition syndrome associated with RUNX1 2024-11-18 criteria provided, single submitter clinical testing
Ambry Genetics RCV004955562 SCV005495330 likely benign Inborn genetic diseases 2024-12-10 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
PreventionGenetics, part of Exact Sciences RCV004742463 SCV005366611 likely benign RUNX1-related disorder 2024-05-17 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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