21-34788755-T-C
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP2BA1
This summary comes from the ClinGen Evidence Repository: The NM_001754.4:c.*3380A>G variant in the 3' UTR has an MAF of 0.08 (8%, 3561/42024 alleles) in the African subpopulation of the gnomAD v3 cohort and is ≥ 0.0015 (0.15%) (BA1). This variant is detected in a homozygous state in 131 individuals in the gnomAD v3 population database (BP2). In summary, this variant meets criteria to be classified as benign. ACMG/AMP criteria applied, as specified by the Myeloid Malignancy Variant Curation Expert Panel for RUNX1: BA1, BP2. LINK:https://erepo.genome.network/evrepo/ui/classification/CA10650413/MONDO:0011071/008
Frequency
Consequence
NM_001754.5 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RUNX1 | NM_001754.5 | c.*3380A>G | 3_prime_UTR_variant | 9/9 | ENST00000675419.1 | NP_001745.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RUNX1 | ENST00000675419.1 | c.*3380A>G | 3_prime_UTR_variant | 9/9 | NM_001754.5 | ENSP00000501943 | A1 | |||
RUNX1 | ENST00000300305.7 | c.*3380A>G | 3_prime_UTR_variant | 8/8 | 1 | ENSP00000300305 | A1 | |||
RUNX1 | ENST00000344691.8 | c.*3380A>G | 3_prime_UTR_variant | 6/6 | 1 | ENSP00000340690 | P4 | |||
RUNX1 | ENST00000437180.5 | c.*3380A>G | 3_prime_UTR_variant | 9/9 | 5 | ENSP00000409227 | A1 |
Frequencies
GnomAD3 genomes AF: 0.0286 AC: 4358AN: 152192Hom.: 150 Cov.: 32
GnomAD4 exome AF: 0.0104 AC: 847AN: 81260Hom.: 28 Cov.: 0 AF XY: 0.00957 AC XY: 358AN XY: 37408
GnomAD4 genome AF: 0.0287 AC: 4368AN: 152310Hom.: 151 Cov.: 32 AF XY: 0.0285 AC XY: 2122AN XY: 74470
ClinVar
Submissions by phenotype
Hereditary thrombocytopenia and hematological cancer predisposition syndrome associated with RUNX1 Benign:2
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Benign, reviewed by expert panel | curation | ClinGen Myeloid Malignancy Variant Curation Expert Panel | Jan 13, 2020 | The NM_001754.4:c.*3380A>G variant in the 3' UTR has an MAF of 0.08 (8%, 3561/42024 alleles) in the African subpopulation of the gnomAD v3 cohort and is =/> 0.0015 (0.15%) (BA1). This variant is detected in a homozygous state in 131 individuals in the gnomAD v3 population database (BP2). In summary, this variant meets criteria to be classified as benign. ACMG/AMP criteria applied, as specified by the Myeloid Malignancy Variant Curation Expert Panel for RUNX1: BA1, BP2. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at