rs2296840
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000495288.5(PSMB4):n.12C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0392 in 1,592,352 control chromosomes in the GnomAD database, including 8,497 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 0.079 ( 1308 hom., cov: 31)
Exomes 𝑓: 0.035 ( 7189 hom. )
Consequence
PSMB4
ENST00000495288.5 non_coding_transcript_exon
ENST00000495288.5 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.680
Genes affected
PSMB4 (HGNC:9541): (proteasome 20S subunit beta 4) 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. [provided by RefSeq, Jul 2008]
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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=-0.54).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.423 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PSMB4 | NM_002796.3 | upstream_gene_variant | ENST00000290541.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PSMB4 | ENST00000290541.7 | upstream_gene_variant | 1 | NM_002796.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0792 AC: 12052AN: 152108Hom.: 1303 Cov.: 31
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GnomAD3 exomes AF: 0.0977 AC: 22553AN: 230762Hom.: 3263 AF XY: 0.0873 AC XY: 11008AN XY: 126046
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GnomAD4 exome AF: 0.0349 AC: 50253AN: 1440126Hom.: 7189 Cov.: 29 AF XY: 0.0352 AC XY: 25248AN XY: 716294
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GnomAD4 genome ? AF: 0.0794 AC: 12090AN: 152226Hom.: 1308 Cov.: 31 AF XY: 0.0864 AC XY: 6433AN XY: 74436
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at