rs764387069
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.300C>G (p.Ser100=) is a synonymous variant. In summary, this variant meets the criteria to be classified as likely benign. Therefore, a REVEL score is not calculable. SpliceAI prediction suggests Acceptor loss 0, Donor loss 0, Acceptor gain 0, Donor gain 0. Therefore, there appears to be no effect on splicing (BP4). Evolutionary conservation prediction algorithms predict the site as not being conserved (PhyloP score -0.302402 < 2.0)(BP7 ). This variant is completely absent from all population databases with at least 20x coverage for RUNX1(PM2_supporting). 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/CA512318845/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.300C>G | p.Ser100= | synonymous_variant | 4/9 | ENST00000675419.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RUNX1 | ENST00000675419.1 | c.300C>G | p.Ser100= | synonymous_variant | 4/9 | NM_001754.5 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152234Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461322Hom.: 0 Cov.: 35 AF XY: 0.00000138 AC XY: 1AN XY: 727006
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152234Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74378
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.300C>G (p.Ser100=) is a synonymous variant. In summary, this variant meets the criteria to be classified as likely benign. Therefore, a REVEL score is not calculable. SpliceAI prediction suggests Acceptor loss 0, Donor loss 0, Acceptor gain 0, Donor gain 0. Therefore, there appears to be no effect on splicing (BP4). Evolutionary conservation prediction algorithms predict the site as not being conserved (PhyloP score -0.302402 < 2.0)(BP7 ). This variant is completely absent from all population databases with at least 20x coverage for RUNX1(PM2_supporting). 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 | Oct 20, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at