rs941718
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000555895.5(PSMB5):c.351+7529A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 1,345,932 control chromosomes in the GnomAD database, including 75,493 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 0.42 ( 17426 hom., cov: 31)
Exomes 𝑓: 0.30 ( 58067 hom. )
Consequence
PSMB5
ENST00000555895.5 intron
ENST00000555895.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.622
Genes affected
PSMB5 (HGNC:9542): (proteasome 20S subunit beta 5) The proteasome is a multicatalytic proteinase complex with a highly ordered ring-shaped 20S core structure. The core structure is composed of 4 rings of 28 non-identical subunits; 2 rings are composed of 7 alpha subunits and 2 rings are composed of 7 beta subunits. Proteasomes are distributed throughout eukaryotic cells at a high concentration and cleave peptides in an ATP/ubiquitin-dependent process in a non-lysosomal pathway. An essential function of a modified proteasome, the immunoproteasome, is the processing of class I MHC peptides. This gene encodes a member of the proteasome B-type family, also known as the T1B family, that is a 20S core beta subunit in the proteasome. This catalytic subunit is not present in the immunoproteasome and is replaced by catalytic subunit 3i (proteasome beta 8 subunit). Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2009]
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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=-0.47).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.772 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PSMB5 | NM_002797.5 | downstream_gene_variant | ENST00000361611.11 | ||||
PSMB5 | NM_001130725.1 | downstream_gene_variant | |||||
PSMB5 | NM_001144932.3 | downstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PSMB5 | ENST00000555895.5 | c.351+7529A>G | intron_variant | 3 | |||||
PSMB5 | ENST00000361611.11 | downstream_gene_variant | 1 | NM_002797.5 | P1 | ||||
PSMB5 | ENST00000493471.2 | downstream_gene_variant | 1 | ||||||
PSMB5 | ENST00000460922.2 | downstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.421 AC: 63892AN: 151930Hom.: 17364 Cov.: 31
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GnomAD4 exome AF: 0.297 AC: 354015AN: 1193884Hom.: 58067 Cov.: 26 AF XY: 0.299 AC XY: 172061AN XY: 575240
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GnomAD4 genome ? AF: 0.421 AC: 64004AN: 152048Hom.: 17426 Cov.: 31 AF XY: 0.416 AC XY: 30918AN XY: 74310
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at