chr21-34859529-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP7BP4
This summary comes from the ClinGen Evidence Repository: NM_001754.5(RUNX1):c.558C>T (p.Val186=) is synonymous variant. No REVEL score because synonymous variant and SpliceAI is ≤0.20 (0.00) meeting BP4 . Evolutionary conservation prediction algorithms predict the site as not being conserved (phyloP -1.3873 < 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/CA320618002/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
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RUNX1 | NM_001754.5 | c.558C>T | p.Val186= | synonymous_variant | 6/9 | ENST00000675419.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RUNX1 | ENST00000675419.1 | c.558C>T | p.Val186= | synonymous_variant | 6/9 | NM_001754.5 | A1 | ||
RUNX1-AS1 | ENST00000651798.1 | n.661+22583G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152198Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461876Hom.: 0 Cov.: 30 AF XY: 0.00000825 AC XY: 6AN XY: 727244
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152198Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74346
ClinVar
Submissions by phenotype
Hereditary thrombocytopenia and hematologic cancer predisposition syndrome Benign:1
Likely benign, reviewed by expert panel | curation | ClinGen Myeloid Malignancy Variant Curation Expert Panel | Feb 10, 2022 | NM_001754.5(RUNX1):c.558C>T (p.Val186=) is synonymous variant. No REVEL score because synonymous variant and SpliceAI is ≤0.20 (0.00) meeting BP4 . Evolutionary conservation prediction algorithms predict the site as not being conserved (phyloP -1.3873 < 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 thrombocytopenia and hematological cancer predisposition syndrome associated with RUNX1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 23, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at