rs11877878

chr18-26184271-A-G

Variant summary

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

The NM_001025096.2(PSMA8):c.660+5141A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 150,318 control chromosomes in the GnomAD database, including 8,751 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 0.23 (8751 hom., cov: 31)
• Consequence: PSMA8 NM_001025096.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.737

Genes affected

PSMA8 (HGNC:22985): (proteasome 20S subunit alpha 8) Predicted to be involved in meiotic cell cycle and proteasomal protein catabolic process. Located in extracellular exosome and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.579 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PSMA8	NM_001025096.2	c.660+5141A>G		intron_variant		ENST00000415576.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PSMA8	ENST00000415576.7	c.660+5141A>G		intron_variant		1	NM_001025096.2	P3

Frequencies

GnomAD3 genomes AF: 0.232 AC: 34896 AN: 150198 Hom.: 8718 Cov.: 31

Gnomad AFR AF: 0.585

Gnomad AMI AF: 0.0607

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.100

Gnomad FIN AF: 0.0927

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0709

Gnomad OTH AF: 0.204

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.233 AC: 34978 AN: 150318 Hom.: 8751 Cov.: 31 AF XY: 0.229 AC XY: 16780 AN XY: 73422

Gnomad4 AFR AF: 0.585

Gnomad4 AMR AF: 0.218

Gnomad4 ASJ AF: 0.117

Gnomad4 EAS AF: 0.165

Gnomad4 SAS AF: 0.100

Gnomad4 FIN AF: 0.0927

Gnomad4 NFE AF: 0.0709

Gnomad4 OTH AF: 0.202

Alfa AF: 0.102 Hom.: 1828

Bravo AF: 0.264

Asia WGS AF: 0.181 AC: 621 AN: 3446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	5.7
Dann	Benign	0.77

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: rs11877878; hg19: chr18-23764235;