rs1979905

chr15-78550032-A-Cchr15-78550032-A-Gchr15-78550032-A-T

Variant summary

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

The NM_002789.6(PSMA4):c.*1088A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.665 in 152,140 control chromosomes in the GnomAD database, including 34,375 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 (34364 hom., cov: 33)
  • Exomes 𝑓: 0.65 (11 hom.)
• Consequence: PSMA4 NM_002789.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.237

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.816 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PSMA4	NM_002789.6	c.*1088A>C		3_prime_UTR_variant	9/9	ENST00000044462.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PSMA4	ENST00000044462.12	c.*1088A>C		3_prime_UTR_variant	9/9	1	NM_002789.6	P1

Frequencies

GnomAD3 genomes AF: 0.665 AC: 101080 AN: 151976 Hom.: 34320 Cov.: 33

Gnomad AFR AF: 0.772

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.745

Gnomad ASJ AF: 0.646

Gnomad EAS AF: 0.836

Gnomad SAS AF: 0.668

Gnomad FIN AF: 0.623

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.674

GnomAD4 exome AF: 0.652 AC: 30 AN: 46 Hom.: 11 Cov.: 0 AF XY: 0.618 AC XY: 21 AN XY: 34

Gnomad4 AMR exome AF: 1.00

Gnomad4 EAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.875

Gnomad4 NFE exome AF: 0.567

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.665 AC: 101183 AN: 152094 Hom.: 34364 Cov.: 33 AF XY: 0.670 AC XY: 49804 AN XY: 74360

Gnomad4 AFR AF: 0.772

Gnomad4 AMR AF: 0.745

Gnomad4 ASJ AF: 0.646

Gnomad4 EAS AF: 0.837

Gnomad4 SAS AF: 0.669

Gnomad4 FIN AF: 0.623

Gnomad4 NFE AF: 0.577

Gnomad4 OTH AF: 0.672

Alfa AF: 0.610 Hom.: 4642

Bravo AF: 0.678

Asia WGS AF: 0.731 AC: 2542 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.6
Dann	Benign	0.73

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: rs1979905; hg19: chr15-78842374;