Variant rs3746651 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_002792.4(PSMA7):c.-61G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.767 in 1,006,390 control chromosomes in the GnomAD database, including 305,654 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 0.63 ( 34017 hom., cov: 33)

Exomes 𝑓: 0.79 ( 271637 hom. )

Consequence

PSMA7
NM_002792.4 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.868

Variant links:

Genes affected

PSMA7 (HGNC:9536): (proteasome 20S subunit alpha 7) 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. 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 peptidase T1A family that functions as a 20S core alpha subunit. The encoded protein interacts with the hepatitis B virus X protein and plays a role in regulating hepatitis C virus internal ribosome entry site (IRES) activity, an activity essential for viral replication. The encoded protein also plays a role in the cellular stress response by regulating hypoxia-inducible factor-1alpha. A pseudogene of this gene is located on the long arm of chromosome 9. [provided by RefSeq, Jul 2012]

PSMA7 links:

PSMA7 (HGNC:):

PSMA7 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=-0.72).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.795 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PSMA7	NM_002792.4 linkuse as main transcript	c.-61G>A		5_prime_UTR_variant	1/7	ENST00000370873.9	NP_002783.1	O14818-1A0A0K0K1K4

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	UniProt
PSMA7	ENST00000370873.9 linkuse as main transcript	c.-61G>A	5_prime_UTR_variant	1/7	1	NM_002792.4	ENSP00000359910.4	O14818-1
PSMA7	ENST00000370858.3 linkuse as main transcript	c.-61G>A	5_prime_UTR_variant	1/3	2		ENSP00000359895.3	O14818-4
PSMA7	ENST00000484488.5 linkuse as main transcript	n.77G>A	non_coding_transcript_exon_variant	1/7	3

Frequencies

GnomAD3 genomes

AF:

0.632

AC:

93880

AN:

148596

Hom.:

34020

Cov.:

show subpopulations

Gnomad AFR

AF:

0.243

Gnomad AMI

AF:

0.877

Gnomad AMR

AF:

0.716

Gnomad ASJ

AF:

0.716

Gnomad EAS

AF:

0.776

Gnomad SAS

AF:

0.738

Gnomad FIN

AF:

0.794

Gnomad MID

AF:

0.782

Gnomad NFE

AF:

0.801

Gnomad OTH

AF:

0.687

GnomAD4 exome

AF:

0.791

AC:

678389

AN:

857688

Hom.:

271637

Cov.:

AF XY:

0.792

AC XY:

330313

AN XY:

416982

show subpopulations

Gnomad4 AFR exome

AF:

0.208

Gnomad4 AMR exome

AF:

0.761

Gnomad4 ASJ exome

AF:

0.743

Gnomad4 EAS exome

AF:

0.828

Gnomad4 SAS exome

AF:

0.771

Gnomad4 FIN exome

AF:

0.810

Gnomad4 NFE exome

AF:

0.805

Gnomad4 OTH exome

AF:

0.767

GnomAD4 genome

AF:

0.631

AC:

93892

AN:

148702

Hom.:

34017

Cov.:

AF XY:

0.635

AC XY:

46007

AN XY:

72506

show subpopulations

Gnomad4 AFR

AF:

0.242

Gnomad4 AMR

AF:

0.716

Gnomad4 ASJ

AF:

0.716

Gnomad4 EAS

AF:

0.775

Gnomad4 SAS

AF:

0.738

Gnomad4 FIN

AF:

0.794

Gnomad4 NFE

AF:

0.801

Gnomad4 OTH

AF:

0.687

Alfa

AF:

0.691

Hom.:

4894

Bravo

AF:

0.613

Asia WGS

AF:

0.691

AC:

2085

AN:

3022

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.72

CADD

Benign

DANN

Benign

0.89

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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