ClinVar Miner

Submissions for variant NM_001754.5(RUNX1):c.552G>T (p.Pro184=)

gnomAD frequency: 0.00006  dbSNP: rs752586117
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ClinGen Myeloid Malignancy Variant Curation Expert Panel RCV001290693 SCV001478830 benign Hereditary thrombocytopenia and hematologic cancer predisposition syndrome 2020-08-24 reviewed by expert panel curation The c.552G>T variant predicts a synonymous change, Pro184= and has an MAF of 0.001654 (0.17%, 33/19954 alleles) in the East Asian subpopulation of the gnomAD v2.1.1 cohort and is ≥ 0.0015 (0.15%) (BA1). This synonymous variant is predicted by SSF and MES to lead to either an increase in the canonical splice site score or a decrease of the canonical splice site score by no more than 10% and no putative cryptic splice sites are created (BP4). In addition, evolutionary conservation prediction algorithms predict the site as not being highly conserved (PhyloP score -8.975 < 0.1) (BP7). In summary, this variant meets criteria to be classified as benign. ACMG/AMP criteria applied, as specified by the Myeloid Malignancy Variant Curation Expert Panel for RUNX1: BA1, BP4, BP7.
Labcorp Genetics (formerly Invitae), Labcorp RCV001088467 SCV000638146 benign Hereditary thrombocytopenia and hematological cancer predisposition syndrome associated with RUNX1 2025-01-30 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV000680419 SCV000807790 likely benign not provided 2017-01-16 criteria provided, single submitter clinical testing
Ambry Genetics RCV004965551 SCV005495310 likely benign Inborn genetic diseases 2024-08-21 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.

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