rs3820667
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000538610.5(PSMA5):c.-608T>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.434 in 153,836 control chromosomes in the GnomAD database, including 16,582 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 0.43 ( 16359 hom., cov: 32)
Exomes 𝑓: 0.50 ( 223 hom. )
Consequence
PSMA5
ENST00000538610.5 5_prime_UTR
ENST00000538610.5 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.293
Genes affected
PSMA5 (HGNC:9534): (proteasome 20S subunit alpha 5) 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 peptidase T1A family, that is a 20S core alpha subunit. Multiple alternatively spliced transcript variants encoding two distinct isoforms have been found for this gene. [provided by RefSeq, Dec 2010]
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=-0.81).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.605 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PSMA5 | NM_002790.4 | c.29+514T>G | intron_variant | ENST00000271308.9 | |||
PSMA5 | NM_001199772.2 | c.-79+514T>G | intron_variant | ||||
PSMA5 | NM_001199773.2 | c.-146+617T>G | intron_variant | ||||
PSMA5 | NM_001199774.2 | c.-146+632T>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PSMA5 | ENST00000538610.5 | c.-608T>G | 5_prime_UTR_variant | 1/9 | 1 | ||||
PSMA5 | ENST00000271308.9 | c.29+514T>G | intron_variant | 1 | NM_002790.4 | P1 | |||
PSMA5 | ENST00000490870.5 | n.345T>G | non_coding_transcript_exon_variant | 1/9 | 1 | ||||
PSMA5 | ENST00000484563.1 | n.126+514T>G | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.433 AC: 65801AN: 151936Hom.: 16351 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
65801
AN:
151936
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.500 AC: 891AN: 1782Hom.: 223 Cov.: 0 AF XY: 0.513 AC XY: 507AN XY: 988
GnomAD4 exome
AF:
AC:
891
AN:
1782
Hom.:
Cov.:
0
AF XY:
AC XY:
507
AN XY:
988
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.433 AC: 65821AN: 152054Hom.: 16359 Cov.: 32 AF XY: 0.435 AC XY: 32349AN XY: 74318
GnomAD4 genome
?
AF:
AC:
65821
AN:
152054
Hom.:
Cov.:
32
AF XY:
AC XY:
32349
AN XY:
74318
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1895
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at