chr15-90749472-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 2P and 16B. PM2BP4_StrongBP6_Very_StrongBS1
The NM_001287248.2(BLM):c.-1088C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000107 in 1,613,030 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001287248.2 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152058Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000247 AC: 62AN: 250996Hom.: 1 AF XY: 0.000294 AC XY: 40AN XY: 135826
GnomAD4 exome AF: 0.000110 AC: 161AN: 1460854Hom.: 1 Cov.: 31 AF XY: 0.000164 AC XY: 119AN XY: 726808
GnomAD4 genome AF: 0.0000789 AC: 12AN: 152176Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74412
ClinVar
Submissions by phenotype
Bloom syndrome Benign:2
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not specified Benign:1
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Hereditary cancer-predisposing syndrome Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at