rs3746651

Variant summary

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

The ENST00000370873.9(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
ENST00000370873.9 5_prime_UTR

Scores

2

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]

Genome browser will be placed here

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
PSMA7NM_002792.4 linkuse as main transcriptc.-61G>A 5_prime_UTR_variant 1/7 ENST00000370873.9 NP_002783.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PSMA7ENST00000370873.9 linkuse as main transcriptc.-61G>A 5_prime_UTR_variant 1/71 NM_002792.4 ENSP00000359910 P1O14818-1
PSMA7ENST00000370858.3 linkuse as main transcriptc.-61G>A 5_prime_UTR_variant 1/32 ENSP00000359895 O14818-4
PSMA7ENST00000484488.5 linkuse as main transcriptn.77G>A non_coding_transcript_exon_variant 1/73

Frequencies

GnomAD3 genomes
AF:
0.632
AC:
93880
AN:
148596
Hom.:
34020
Cov.:
33
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.:
11
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.:
33
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
14
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.

Other links and lift over

dbSNP: rs3746651; hg19: chr20-60718420; COSMIC: COSV105236232; COSMIC: COSV105236232; API