rs10512488
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001313998.2(BECN1):c.1042-89C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 1,480,016 control chromosomes in the GnomAD database, including 40,723 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.17 ( 3065 hom., cov: 32)
Exomes 𝑓: 0.23 ( 37658 hom. )
Consequence
BECN1
NM_001313998.2 intron
NM_001313998.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.132
Genes affected
BECN1 (HGNC:1034): (beclin 1) This gene encodes a protein that regulates autophagy, a catabolic process of degradation induced by starvation. The encoded protein is a component of the phosphatidylinositol-3-kinase (PI3K) complex which mediates vesicle-trafficking processes. This protein is thought to play a role in multiple cellular processes, including tumorigenesis, neurodegeneration and apoptosis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.249 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BECN1 | NM_001313998.2 | c.1042-89C>T | intron_variant | ENST00000590099.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BECN1 | ENST00000590099.6 | c.1042-89C>T | intron_variant | 1 | NM_001313998.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.174 AC: 26519AN: 152052Hom.: 3068 Cov.: 32
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GnomAD4 exome AF: 0.230 AC: 304926AN: 1327846Hom.: 37658 Cov.: 20 AF XY: 0.227 AC XY: 149205AN XY: 656332
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GnomAD4 genome ? AF: 0.174 AC: 26503AN: 152170Hom.: 3065 Cov.: 32 AF XY: 0.172 AC XY: 12777AN XY: 74402
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at