Variant 6-32844751-C-T 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.-10+477C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 309,492 control chromosomes in the GnomAD database, including 5,100 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.14 ( 1941 hom., cov: 32)

Exomes 𝑓: 0.18 ( 3159 hom. )

Consequence

PSMB9
ENST00000395330.5 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -3.84

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:

PSMB8-AS1 (HGNC:):

PSMB8-AS1 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=-0.76).

BP6

Variant 6-32844751-C-T is Benign according to our data. Variant chr6-32844751-C-T is described in ClinVar as [Benign]. Clinvar id is 1275279.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons
PSMB8-AS1	NR_037173.1 linkuse as main transcript	n.296C>T	non_coding_transcript_exon_variant	2/3
PSMB8-AS1	NR_037174.1 linkuse as main transcript	n.189+477C>T	intron_variant
PSMB8-AS1	NR_037175.1 linkuse as main transcript	n.190-59C>T	intron_variant
PSMB8-AS1	NR_037176.1 linkuse as main transcript	n.189+477C>T	intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	Protein	UniProt
PSMB9	ENST00000395330.5 linkuse as main transcript	c.-10+477C>T	intron_variant		3	ENSP00000378739.1	A2ACR1
PSMB8-AS1	ENST00000412095.1 linkuse as main transcript	n.618C>T	non_coding_transcript_exon_variant	1/2	2
PSMB8-AS1	ENST00000429600.2 linkuse as main transcript	n.304C>T	non_coding_transcript_exon_variant	2/3	2

Frequencies

GnomAD3 genomes

AF:

0.144

AC:

21850

AN:

152114

Hom.:

1940

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0469

Gnomad AMI

AF:

0.0681

Gnomad AMR

AF:

0.204

Gnomad ASJ

AF:

0.188

Gnomad EAS

AF:

0.266

Gnomad SAS

AF:

0.242

Gnomad FIN

AF:

0.149

Gnomad MID

AF:

0.203

Gnomad NFE

AF:

0.170

Gnomad OTH

AF:

0.139

GnomAD4 exome

AF:

0.184

AC:

28950

AN:

157260

Hom.:

3159

Cov.:

AF XY:

0.189

AC XY:

15647

AN XY:

82584

show subpopulations

Gnomad4 AFR exome

AF:

0.0471

Gnomad4 AMR exome

AF:

0.212

Gnomad4 ASJ exome

AF:

0.197

Gnomad4 EAS exome

AF:

0.301

Gnomad4 SAS exome

AF:

0.244

Gnomad4 FIN exome

AF:

0.150

Gnomad4 NFE exome

AF:

0.168

Gnomad4 OTH exome

AF:

0.169

GnomAD4 genome

AF:

0.144

AC:

21861

AN:

152232

Hom.:

1941

Cov.:

AF XY:

0.148

AC XY:

10992

AN XY:

74414

show subpopulations

Gnomad4 AFR

AF:

0.0468

Gnomad4 AMR

AF:

0.204

Gnomad4 ASJ

AF:

0.188

Gnomad4 EAS

AF:

0.266

Gnomad4 SAS

AF:

0.242

Gnomad4 FIN

AF:

0.149

Gnomad4 NFE

AF:

0.171

Gnomad4 OTH

AF:

0.143

Alfa

AF:

0.165

Hom.:

4025

Bravo

AF:

0.140

Asia WGS

AF:

0.285

AC:

989

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 15, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

0.025

DANN

Benign

0.85

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