Variant 17-39997622-T-A details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_002809.4(PSMD3):c.*41T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 1,468,704 control chromosomes in the GnomAD database, including 102,174 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 0.36 ( 9807 hom., cov: 32)

Exomes 𝑓: 0.36 ( 92367 hom. )

Consequence

PSMD3
NM_002809.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.53

Variant links:

Genes affected

PSMD3 (HGNC:9560): (proteasome 26S subunit, non-ATPase 3) 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 member of the proteasome subunit S3 family that functions as one of the non-ATPase subunits of the 19S regulator lid. Single nucleotide polymorphisms in this gene are associated with neutrophil count. [provided by RefSeq, Jul 2012]

PSMD3 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=-0.58).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PSMD3	NM_002809.4 linkuse as main transcript	c.*41T>A		3_prime_UTR_variant	12/12	ENST00000264639.9	NP_002800.2

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PSMD3	ENST00000264639.9 linkuse as main transcript	c.*41T>A	3_prime_UTR_variant	12/12	1	NM_002809.4	ENSP00000264639	P1	O43242-1
PSMD3	ENST00000540504.2 linkuse as main transcript	c.297-172T>A	intron_variant		3		ENSP00000444980
PSMD3	ENST00000415039.7 linkuse as main transcript		downstream_gene_variant		2		ENSP00000407410

Frequencies

GnomAD3 genomes

AF:

0.356

AC:

54097

AN:

151896

Hom.:

9794

Cov.:

show subpopulations

Gnomad AFR

AF:

0.297

Gnomad AMI

AF:

0.423

Gnomad AMR

AF:

0.335

Gnomad ASJ

AF:

0.348

Gnomad EAS

AF:

0.460

Gnomad SAS

AF:

0.254

Gnomad FIN

AF:

0.396

Gnomad MID

AF:

0.222

Gnomad NFE

AF:

0.391

Gnomad OTH

AF:

0.333

GnomAD3 exomes

AF:

0.361

AC:

84134

AN:

233054

Hom.:

15304

AF XY:

0.357

AC XY:

45515

AN XY:

127362

show subpopulations

Gnomad AFR exome

AF:

0.301

Gnomad AMR exome

AF:

0.326

Gnomad ASJ exome

AF:

0.335

Gnomad EAS exome

AF:

0.476

Gnomad SAS exome

AF:

0.259

Gnomad FIN exome

AF:

0.386

Gnomad NFE exome

AF:

0.388

Gnomad OTH exome

AF:

0.349

GnomAD4 exome

AF:

0.357

AC:

470483

AN:

1316690

Hom.:

92367

Cov.:

AF XY:

0.355

AC XY:

234212

AN XY:

660174

show subpopulations

Gnomad4 AFR exome

AF:

0.275

Gnomad4 AMR exome

AF:

0.330

Gnomad4 ASJ exome

AF:

0.335

Gnomad4 EAS exome

AF:

0.490

Gnomad4 SAS exome

AF:

0.254

Gnomad4 FIN exome

AF:

0.388

Gnomad4 NFE exome

AF:

0.364

Gnomad4 OTH exome

AF:

0.361

GnomAD4 genome

AF:

0.356

AC:

54165

AN:

152014

Hom.:

9807

Cov.:

AF XY:

0.355

AC XY:

26356

AN XY:

74334

show subpopulations

Gnomad4 AFR

AF:

0.297

Gnomad4 AMR

AF:

0.337

Gnomad4 ASJ

AF:

0.348

Gnomad4 EAS

AF:

0.460

Gnomad4 SAS

AF:

0.255

Gnomad4 FIN

AF:

0.396

Gnomad4 NFE

AF:

0.391

Gnomad4 OTH

AF:

0.335

Alfa

AF:

0.369

Hom.:

1936

Bravo

AF:

0.350

Asia WGS

AF:

0.375

AC:

1302

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.58

CADD

Benign

DANN

Benign

0.70

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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