Variant rs2071480 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The ENST00000395330.5(PSMB9):c.-9-2056C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.412 in 999,508 control chromosomes in the GnomAD database, including 86,152 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.42 ( 13411 hom., cov: 32)

Exomes 𝑓: 0.41 ( 72741 hom. )

Consequence

PSMB9
ENST00000395330.5 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.645

Variant links:

Genes affected

PSMB9 (HGNC:9546): (proteasome 20S subunit beta 9) 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. This gene is located in the class II region of the MHC (major histocompatibility complex). Expression of this gene is induced by gamma interferon and this gene product replaces catalytic subunit 1 (proteasome beta 6 subunit) in the immunoproteasome. Proteolytic processing is required to generate a mature subunit. [provided by RefSeq, Mar 2010]

PSMB9 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.66).

BP6

Variant 6-32854082-C-A is Benign according to our data. Variant chr6-32854082-C-A is described in ClinVar as [Benign]. Clinvar id is 1170127.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.436 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PSMB9	ENST00000395330.5 linkuse as main transcript	c.-9-2056C>A		intron_variant		3		ENSP00000378739
PSMB9	ENST00000414474.5 linkuse as main transcript	c.-9-2056C>A		intron_variant		5		ENSP00000394363

Frequencies

GnomAD3 genomes

AF:

0.418

AC:

63423

AN:

151866

Hom.:

13391

Cov.:

show subpopulations

Gnomad AFR

AF:

0.441

Gnomad AMI

AF:

0.386

Gnomad AMR

AF:

0.413

Gnomad ASJ

AF:

0.447

Gnomad EAS

AF:

0.355

Gnomad SAS

AF:

0.388

Gnomad FIN

AF:

0.368

Gnomad MID

AF:

0.516

Gnomad NFE

AF:

0.417

Gnomad OTH

AF:

0.427

GnomAD4 exome

AF:

0.411

AC:

348305

AN:

847524

Hom.:

72741

Cov.:

AF XY:

0.411

AC XY:

175987

AN XY:

428640

show subpopulations

Gnomad4 AFR exome

AF:

0.439

Gnomad4 AMR exome

AF:

0.422

Gnomad4 ASJ exome

AF:

0.458

Gnomad4 EAS exome

AF:

0.357

Gnomad4 SAS exome

AF:

0.383

Gnomad4 FIN exome

AF:

0.380

Gnomad4 NFE exome

AF:

0.415

Gnomad4 OTH exome

AF:

0.426

GnomAD4 genome

AF:

0.418

AC:

63488

AN:

151984

Hom.:

13411

Cov.:

AF XY:

0.414

AC XY:

30741

AN XY:

74298

show subpopulations

Gnomad4 AFR

AF:

0.442

Gnomad4 AMR

AF:

0.414

Gnomad4 ASJ

AF:

0.447

Gnomad4 EAS

AF:

0.356

Gnomad4 SAS

AF:

0.387

Gnomad4 FIN

AF:

0.368

Gnomad4 NFE

AF:

0.417

Gnomad4 OTH

AF:

0.426

Alfa

AF:

0.351

Hom.:

1436

Bravo

AF:

0.421

Asia WGS

AF:

0.421

AC:

1468

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

MHC class I deficiency

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 02, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.66

CADD

Benign

DANN

Benign

0.62

Splicing

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over