rs9923349
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001079514.3(UBN1):c.249+1957A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.564 in 151,416 control chromosomes in the GnomAD database, including 25,585 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 0.56 ( 25585 hom., cov: 30)
Consequence
UBN1
NM_001079514.3 intron
NM_001079514.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0210
Genes affected
UBN1 (HGNC:12506): (ubinuclein 1) Cellular senescence is a hallmark of tumor suppression and tissue aging. Senescent cells contain domains of heterochromatin, called senescence-associated heterochromatin foci (SAHF), that repress proliferation-promoting genes. The protein encoded by this gene binds to proliferation-promoting genes and is required for SAHF formation, enhancing methylation of histone H3. [provided by RefSeq, Oct 2016]
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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=-0.96).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.765 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
UBN1 | NM_001079514.3 | c.249+1957A>G | intron_variant | ENST00000262376.11 | NP_001072982.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
UBN1 | ENST00000262376.11 | c.249+1957A>G | intron_variant | 1 | NM_001079514.3 | ENSP00000262376.5 | ||||
UBN1 | ENST00000396658.8 | c.249+1957A>G | intron_variant | 1 | ENSP00000379894.3 | |||||
UBN1 | ENST00000590769.5 | c.249+1957A>G | intron_variant | 2 | ENSP00000468740.1 | |||||
UBN1 | ENST00000592120.5 | c.249+1957A>G | intron_variant | 2 | ENSP00000467942.1 |
Frequencies
GnomAD3 genomes AF: 0.564 AC: 85271AN: 151298Hom.: 25531 Cov.: 30
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.564 AC: 85382AN: 151416Hom.: 25585 Cov.: 30 AF XY: 0.562 AC XY: 41570AN XY: 73944
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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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