chr21-34792267-G-C
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 1P and 2B. BP7PM2_SupportingBP4
This summary comes from the ClinGen Evidence Repository: NM_001754.5(RUNX1):c.1311C>G (p.Thr437=) is s synonymous variant. Computation evidence is not calculable for the effect of this SYNONYMOUS variant on protein function. The REVEL score is not calculable. Splice AI predicts a 0.00 score for acceptor loss, donor loss, acceptor gain, and donor gain(BP4). Evolutionary conservation prediction algorithms predict the site as not being conserved (PhyloP score -3.62398 < 2.0)(BP7). This synonymous variant is absent from all examined population databases with at least 20x coverage for RUNX1(PM2_supporting). 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, BP7, PM2_supporting LINK:https://erepo.genome.network/evrepo/ui/classification/CA512341068/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 -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RUNX1 | NM_001754.5 | c.1311C>G | p.Thr437= | synonymous_variant | 9/9 | ENST00000675419.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RUNX1 | ENST00000675419.1 | c.1311C>G | p.Thr437= | synonymous_variant | 9/9 | NM_001754.5 | A1 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome AF: 0.00000865 AC: 12AN: 1387542Hom.: 0 Cov.: 33 AF XY: 0.00000876 AC XY: 6AN XY: 684836
GnomAD4 genome Cov.: 31
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 | Jul 07, 2022 | NM_001754.5(RUNX1):c.1311C>G (p.Thr437=) is s synonymous variant. Computation evidence is not calculable for the effect of this SYNONYMOUS variant on protein function. The REVEL score is not calculable. Splice AI predicts a 0.00 score for acceptor loss, donor loss, acceptor gain, and donor gain(BP4). Evolutionary conservation prediction algorithms predict the site as not being conserved (PhyloP score -3.62398 < 2.0)(BP7). This synonymous variant is absent from all examined population databases with at least 20x coverage for RUNX1(PM2_supporting). 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, BP7, PM2_supporting - |
Hereditary thrombocytopenia and hematological cancer predisposition syndrome associated with RUNX1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 24, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at