Variant 9-120824459-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_005047.4(PSMD5):c.1006+35A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.577 in 1,601,154 control chromosomes in the GnomAD database, including 274,835 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 0.49 ( 20646 hom., cov: 32)

Exomes 𝑓: 0.59 ( 254189 hom. )

Consequence

PSMD5
NM_005047.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.114

Variant links:

Genes affected

PSMD5 (HGNC:9563): (proteasome 26S subunit, non-ATPase 5) The 26S proteasome is a multicatalytic proteinase complex with a highly ordered structure composed of 2 complexes, a 20S core and a 19S regulator. The 20S core 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. The 19S regulator is composed of a base, which contains 6 ATPase subunits and 2 non-ATPase subunits, and a lid, which contains up to 10 non-ATPase 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. This gene encodes a non-ATPase subunit of the 19S regulator base that functions as a chaperone protein during 26S proteasome assembly. [provided by RefSeq, Jul 2012]

PSMD5 links:

PSMD5 (HGNC:):

PSMD5 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=-0.78).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.716 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PSMD5	NM_005047.4 linkuse as main transcript	c.1006+35A>C		intron_variant		ENST00000210313.8	NP_005038.1	Q16401-1
PSMD5	NM_001270427.2 linkuse as main transcript	c.877+35A>C		intron_variant			NP_001257356.1	Q16401-2

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	UniProt
PSMD5	ENST00000210313.8 linkuse as main transcript	c.1006+35A>C	intron_variant		1	NM_005047.4	ENSP00000210313.2	Q16401-1
PSMD5	ENST00000373904.5 linkuse as main transcript	c.877+35A>C	intron_variant		2		ENSP00000363011.5	Q16401-2
PSMD5	ENST00000373920.6 linkuse as main transcript	c.25+35A>C	intron_variant		5		ENSP00000363030.2	Q4VXH0
PSMD5	ENST00000373903.1 linkuse as main transcript	n.357A>C	non_coding_transcript_exon_variant	2/2	3

Frequencies

GnomAD3 genomes

AF:

0.491

AC:

74645

AN:

151908

Hom.:

20633

Cov.:

show subpopulations

Gnomad AFR

AF:

0.222

Gnomad AMI

AF:

0.398

Gnomad AMR

AF:

0.629

Gnomad ASJ

AF:

0.653

Gnomad EAS

AF:

0.477

Gnomad SAS

AF:

0.734

Gnomad FIN

AF:

0.588

Gnomad MID

AF:

0.617

Gnomad NFE

AF:

0.584

Gnomad OTH

AF:

0.538

GnomAD3 exomes

AF:

0.593

AC:

148303

AN:

250076

Hom.:

46019

AF XY:

0.604

AC XY:

81737

AN XY:

135320

show subpopulations

Gnomad AFR exome

AF:

0.210

Gnomad AMR exome

AF:

0.718

Gnomad ASJ exome

AF:

0.655

Gnomad EAS exome

AF:

0.483

Gnomad SAS exome

AF:

0.732

Gnomad FIN exome

AF:

0.585

Gnomad NFE exome

AF:

0.586

Gnomad OTH exome

AF:

0.594

GnomAD4 exome

AF:

0.586

AC:

849589

AN:

1449128

Hom.:

254189

Cov.:

AF XY:

0.592

AC XY:

427505

AN XY:

721754

show subpopulations

Gnomad4 AFR exome

AF:

0.204

Gnomad4 AMR exome

AF:

0.710

Gnomad4 ASJ exome

AF:

0.647

Gnomad4 EAS exome

AF:

0.427

Gnomad4 SAS exome

AF:

0.737

Gnomad4 FIN exome

AF:

0.589

Gnomad4 NFE exome

AF:

0.586

Gnomad4 OTH exome

AF:

0.572

GnomAD4 genome

AF:

0.491

AC:

74677

AN:

152026

Hom.:

20646

Cov.:

AF XY:

0.499

AC XY:

37107

AN XY:

74304

show subpopulations

Gnomad4 AFR

AF:

0.222

Gnomad4 AMR

AF:

0.629

Gnomad4 ASJ

AF:

0.653

Gnomad4 EAS

AF:

0.477

Gnomad4 SAS

AF:

0.736

Gnomad4 FIN

AF:

0.588

Gnomad4 NFE

AF:

0.584

Gnomad4 OTH

AF:

0.538

Alfa

AF:

0.578

Hom.:

59882

Bravo

AF:

0.480

Asia WGS

AF:

0.582

AC:

2026

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

6.3

DANN

Benign

0.66

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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