Variant rs2296840 details in Genebe, Genetics Data Aggregator

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.680

Variant links:

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]

PSMB4 links:

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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	Protein	UniProt
PSMB4	NM_002796.3 linkuse as main transcript			upstream_gene_variant		ENST00000290541.7	NP_002787.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PSMB4	ENST00000290541.7 linkuse as main transcript			upstream_gene_variant		1	NM_002796.3	ENSP00000290541	P1

Frequencies

GnomAD3 genomes

AF:

0.0792

AC:

12052

AN:

152108

Hom.:

1303

Cov.:

show subpopulations

Gnomad AFR

AF:

0.116

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.211

Gnomad ASJ

AF:

0.00662

Gnomad EAS

AF:

0.438

Gnomad SAS

AF:

0.108

Gnomad FIN

AF:

0.0758

Gnomad MID

AF:

0.0222

Gnomad NFE

AF:

0.00369

Gnomad OTH

AF:

0.0703

GnomAD3 exomes

AF:

0.0977

AC:

22553

AN:

230762

Hom.:

3263

AF XY:

0.0873

AC XY:

11008

AN XY:

126046

show subpopulations

Gnomad AFR exome

AF:

0.121

Gnomad AMR exome

AF:

0.315

Gnomad ASJ exome

AF:

0.0104

Gnomad EAS exome

AF:

0.404

Gnomad SAS exome

AF:

0.0929

Gnomad FIN exome

AF:

0.0703

Gnomad NFE exome

AF:

0.00465

Gnomad OTH exome

AF:

0.0725

GnomAD4 exome

AF:

0.0349

AC:

50253

AN:

1440126

Hom.:

7189

Cov.:

AF XY:

0.0352

AC XY:

25248

AN XY:

716294

show subpopulations

Gnomad4 AFR exome

AF:

0.125

Gnomad4 AMR exome

AF:

0.299

Gnomad4 ASJ exome

AF:

0.00939

Gnomad4 EAS exome

AF:

0.453

Gnomad4 SAS exome

AF:

0.0884

Gnomad4 FIN exome

AF:

0.0647

Gnomad4 NFE exome

AF:

0.00245

Gnomad4 OTH exome

AF:

0.0564

GnomAD4 genome

AF:

0.0794

AC:

12090

AN:

152226

Hom.:

1308

Cov.:

AF XY:

0.0864

AC XY:

6433

AN XY:

74436

show subpopulations

Gnomad4 AFR

AF:

0.117

Gnomad4 AMR

AF:

0.211

Gnomad4 ASJ

AF:

0.00662

Gnomad4 EAS

AF:

0.438

Gnomad4 SAS

AF:

0.109

Gnomad4 FIN

AF:

0.0758

Gnomad4 NFE

AF:

0.00371

Gnomad4 OTH

AF:

0.0734

Alfa

AF:

0.0289

Hom.:

842

Bravo

AF:

0.0933

Asia WGS

AF:

0.271

AC:

941

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.54

CADD

Benign

DANN

Benign

0.94

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over