chr21-34788158-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1
This summary comes from the ClinGen Evidence Repository: The c.*3977G>A variant in the 3' UTR has an MAF of 0.003831 (0.38%, 12/3132 alleles) in the East Asian subpopulation of the gnomAD v3 cohort and is ≥ 0.0015 (0.15%) (BA1). 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. LINK:https://erepo.genome.network/evrepo/ui/classification/CA10650402/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 -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RUNX1 | NM_001754.5 | c.*3977G>A | 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.*3977G>A | 3_prime_UTR_variant | 9/9 | NM_001754.5 | ENSP00000501943 | A1 | |||
RUNX1 | ENST00000300305.7 | c.*3977G>A | 3_prime_UTR_variant | 8/8 | 1 | ENSP00000300305 | A1 | |||
RUNX1 | ENST00000344691.8 | c.*3977G>A | 3_prime_UTR_variant | 6/6 | 1 | ENSP00000340690 | P4 | |||
RUNX1 | ENST00000437180.5 | c.*3977G>A | 3_prime_UTR_variant | 9/9 | 5 | ENSP00000409227 | A1 |
Frequencies
GnomAD3 genomes AF: 0.000164 AC: 25AN: 152208Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.000358 AC: 29AN: 81110Hom.: 0 Cov.: 0 AF XY: 0.000375 AC XY: 14AN XY: 37310
GnomAD4 genome AF: 0.000158 AC: 24AN: 152326Hom.: 0 Cov.: 32 AF XY: 0.000174 AC XY: 13AN XY: 74500
ClinVar
Submissions by phenotype
Hereditary thrombocytopenia and hematologic cancer predisposition syndrome Benign:1
Benign, reviewed by expert panel | curation | ClinGen Myeloid Malignancy Variant Curation Expert Panel | May 13, 2020 | The c.*3977G>A variant in the 3' UTR has an MAF of 0.003831 (0.38%, 12/3132 alleles) in the East Asian subpopulation of the gnomAD v3 cohort and is >= 0.0015 (0.15%) (BA1). 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. - |
Hereditary thrombocytopenia and hematological cancer predisposition syndrome associated with RUNX1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at