21-34792091-G-C
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP2BA1
This summary comes from the ClinGen Evidence Repository: NM_001754.5(RUNX1):c.*44C>G is a 3' UTR variant. MAF of 0.01 (1.31%, 885/67420 alleles) in the European (non-Finnish) subpopulation of the gnomAD v3.1.2 cohort is ≥ 0.0015 (0.15%) (BA1). This variant is reported in 4 homozygotes in gnomAD v3.1.2 (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/CA10014163/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
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00852 AC: 1281AN: 150344Hom.: 4 Cov.: 32
GnomAD3 exomes AF: 0.0109 AC: 59AN: 5428Hom.: 0 AF XY: 0.0112 AC XY: 39AN XY: 3478
GnomAD4 exome AF: 0.0124 AC: 13700AN: 1104612Hom.: 110 Cov.: 17 AF XY: 0.0123 AC XY: 6571AN XY: 536204
GnomAD4 genome AF: 0.00852 AC: 1282AN: 150452Hom.: 4 Cov.: 32 AF XY: 0.00834 AC XY: 613AN XY: 73504
ClinVar
Submissions by phenotype
not provided Benign:2
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not specified Benign:1
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Hereditary thrombocytopenia and hematologic cancer predisposition syndrome Benign:1
NM_001754.5(RUNX1):c.*44C>G is a 3' UTR variant. MAF of 0.01 (1.31%, 885/67420 alleles) in the European (non-Finnish) subpopulation of the gnomAD v3.1.2 cohort is ≥ 0.0015 (0.15%) (BA1). This variant is reported in 4 homozygotes in gnomAD v3.1.2 (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 -
Hereditary thrombocytopenia and hematological cancer predisposition syndrome associated with RUNX1 Benign:1
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. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at