rs7164030

chr15-78552319-G-Achr15-78552319-G-Cchr15-78552319-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002789.6(PSMA4):c.*3375G>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 0.667 in 152,080 control chromosomes in the GnomAD database, including 34,535 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 0.67 (34535 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: PSMA4 NM_002789.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.101

Genes affected

PSMA4 (HGNC:9533): (proteasome 20S subunit alpha 4) This gene encodes a core alpha subunit of the 20S proteosome, which is a highly ordered ring-shaped structure composed of four rings of 28 non-identical subunits. Proteasomes cleave peptides in an ATP- and ubiquitin-dependent manner. [provided by RefSeq, Aug 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.815 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PSMA4	NM_002789.6	c.*3375G>A		3_prime_UTR_variant	9/9	ENST00000044462.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PSMA4	ENST00000044462.12	c.*3375G>A		3_prime_UTR_variant	9/9	1	NM_002789.6	P1

Frequencies

GnomAD3 genomes AF: 0.667 AC: 101297 AN: 151962 Hom.: 34491 Cov.: 33

Gnomad AFR AF: 0.773

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.759

Gnomad ASJ AF: 0.646

Gnomad EAS AF: 0.835

Gnomad SAS AF: 0.665

Gnomad FIN AF: 0.620

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.677

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.667 AC: 101400 AN: 152080 Hom.: 34535 Cov.: 33 AF XY: 0.671 AC XY: 49873 AN XY: 74328

Gnomad4 AFR AF: 0.773

Gnomad4 AMR AF: 0.760

Gnomad4 ASJ AF: 0.646

Gnomad4 EAS AF: 0.835

Gnomad4 SAS AF: 0.666

Gnomad4 FIN AF: 0.620

Gnomad4 NFE AF: 0.577

Gnomad4 OTH AF: 0.675

Alfa AF: 0.495 Hom.: 1422

Bravo AF: 0.681

Asia WGS AF: 0.730 AC: 2540 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	1.2
Dann	Benign	0.64

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

Other links and lift over

dbSNP: rs7164030; hg19: chr15-78844661;