21-34859467-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4BP7
This summary comes from the ClinGen Evidence Repository: This c.613+7G>A intronic variant is located at a weakly conserved nucleotide per an evolutionary conservation prediction algorithm (PhyloP score = 1.15676 in GRCh38); it is not predicted to have any splicing impact per SpliceAI (Δ scores ≤ 0.20) (BP7+BP4). In summary, this variant meets criteria to be classified as likely benign. ACMG/AMP criteria applied, as specified by the ClinGen Myeloid Malignancy Variant Curation Expert Panel for RUNX1: BP4 and BP7. LINK:https://erepo.genome.network/evrepo/ui/classification/CA637745016/MONDO:0011071/008
Frequency
Consequence
NM_001754.5 splice_region, intron
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 Cov.: 33
GnomAD3 exomes AF: 0.00000795 AC: 2AN: 251474Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135910
GnomAD4 exome AF: 0.00000623 AC: 9AN: 1444050Hom.: 0 Cov.: 29 AF XY: 0.00000556 AC XY: 4AN XY: 719612
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Hereditary thrombocytopenia and hematologic cancer predisposition syndrome Benign:1
This c.613+7G>A intronic variant is located at a weakly conserved nucleotide per an evolutionary conservation prediction algorithm (PhyloP score = 1.15676 in GRCh38); it is not predicted to have any splicing impact per SpliceAI (Δ scores ≤ 0.20) (BP7+BP4). In summary, this variant meets criteria to be classified as likely benign. ACMG/AMP criteria applied, as specified by the ClinGen Myeloid Malignancy Variant Curation Expert Panel for RUNX1: BP4 and BP7. -
Hereditary thrombocytopenia and hematological cancer predisposition syndrome associated with RUNX1 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at