Submissions for variant NM_001754.5(RUNX1):c.303G>T (p.Val101=)

gnomAD frequency: 0.00200  dbSNP: rs142472642

Total submissions: 7

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
ClinGen Myeloid Malignancy Variant Curation Expert Panel	RCV004595497	SCV005088364	benign	Hereditary thrombocytopenia and hematologic cancer predisposition syndrome	2024-06-24	reviewed by expert panel	curation	NM_001754.5(RUNX1):c.303G>T (p.Val101=) is a synonymous variant. MAF of 0.00671 (0.671%, 167/24878, 167 alleles) in the African subpopulation of the gnomAD cohort is ≥ 0.0015 (0.15%) (BA1). Not a missense variant, therefore, no REVEL score and SpliceAI is ≤0.50 (0.00) (BP4). Evolutionary conservation prediction algorithms predict the site as not being conserved (PhyloP score 1.4739 < 2.0 or the variant is the reference nucleotide in one primate and/or three mammal species) (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.
Invitae	RCV000233456	SCV000287184	benign	Hereditary thrombocytopenia and hematological cancer predisposition syndrome associated with RUNX1	2024-01-25	criteria provided, single submitter	clinical testing
Illumina Laboratory Services, Illumina	RCV000233456	SCV000435951	likely benign	Hereditary thrombocytopenia and hematological cancer predisposition syndrome associated with RUNX1	2017-04-28	criteria provided, single submitter	clinical testing	This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.
PreventionGenetics, part of Exact Sciences	RCV000680400	SCV000807771	likely benign	not provided	2016-05-04	criteria provided, single submitter	clinical testing
Genetic Services Laboratory, University of Chicago	RCV001818592	SCV002067882	benign	not specified	2019-06-14	criteria provided, single submitter	clinical testing
Sema4, Sema4	RCV002256142	SCV002535859	benign	Hereditary cancer-predisposing syndrome	2020-10-22	criteria provided, single submitter	curation
KCCC/NGS Laboratory, Kuwait Cancer Control Center	RCV003316252	SCV004015361	benign	Acute myeloid leukemia	2023-07-07	criteria provided, single submitter	clinical testing