rs200907577
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4BP7
This summary comes from the ClinGen Evidence Repository: NM_001754.5(RUNX1):c.492C>T (p.Val164=) is a synonymous variant. No REVEL score because a synonymous variant and SpliceAI is ≤0.20( 0.01 Donor Loss -16bp and 0.11 Donor Gain 7bp) (BP4). Evolutionary conservation prediction algorithms predict the site as not being conserved (PhyloP 1.91014 ≤ 2.0) meeting 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: BP4 and BP7. LINK:https://erepo.genome.network/evrepo/ui/classification/CA10014503/MONDO:0011071/008
Frequency
Consequence
NM_001754.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152110Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000103 AC: 26AN: 251404Hom.: 0 AF XY: 0.000118 AC XY: 16AN XY: 135882
GnomAD4 exome AF: 0.0000493 AC: 72AN: 1461806Hom.: 0 Cov.: 31 AF XY: 0.0000454 AC XY: 33AN XY: 727206
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152110Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74298
ClinVar
Submissions by phenotype
not specified Uncertain:1
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Hereditary thrombocytopenia and hematologic cancer predisposition syndrome Benign:1
NM_001754.5(RUNX1):c.492C>T (p.Val164=) is a synonymous variant. No REVEL score because a synonymous variant and SpliceAI is ≤0.20( 0.01 Donor Loss -16bp and 0.11 Donor Gain 7bp) (BP4). Evolutionary conservation prediction algorithms predict the site as not being conserved (PhyloP 1.91014 ≤ 2.0) meeting 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: BP4 and BP7. -
Hereditary cancer-predisposing syndrome Benign:1
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Hereditary thrombocytopenia and hematological cancer predisposition syndrome associated with RUNX1 Benign:1
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Acute myeloid leukemia Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at