rs1045643
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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.*1380C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.137 in 152,098 control chromosomes in the GnomAD database, including 1,603 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 0.14 ( 1603 hom., cov: 31)
Exomes 𝑓: 0.094 ( 0 hom. )
Consequence
UBN1
NM_001079514.3 3_prime_UTR
NM_001079514.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.612
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=-0.85).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.22 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UBN1 | NM_001079514.3 | c.*1380C>T | 3_prime_UTR_variant | 18/18 | ENST00000262376.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UBN1 | ENST00000262376.11 | c.*1380C>T | 3_prime_UTR_variant | 18/18 | 1 | NM_001079514.3 | P4 | ||
UBN1 | ENST00000396658.8 | c.*1380C>T | 3_prime_UTR_variant | 17/17 | 1 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.137 AC: 20765AN: 151948Hom.: 1589 Cov.: 31
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GnomAD4 exome AF: 0.0938 AC: 3AN: 32Hom.: 0 Cov.: 0 AF XY: 0.150 AC XY: 3AN XY: 20
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GnomAD4 genome ? AF: 0.137 AC: 20815AN: 152066Hom.: 1603 Cov.: 31 AF XY: 0.138 AC XY: 10222AN XY: 74328
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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