rs11877878

Variant names:

• chr18-26184271-A-G
• rs11877878
• NM_001025096.2:c.660+5141A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001025096.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PSMA8	NM_001025096.2	MANE Select	c.660+5141A>G		intron	N/A	NP_001020267.1
	PSMA8	NM_144662.3		c.678+5141A>G		intron	N/A	NP_653263.2
	PSMA8	NM_001308188.2		c.582+5141A>G		intron	N/A	NP_001295117.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PSMA8	ENST00000415576.7	TSL:1 MANE Select	c.660+5141A>G		intron	N/A	ENSP00000409284.2
	PSMA8	ENST00000308268.10	TSL:1	c.678+5141A>G		intron	N/A	ENSP00000311121.6
	PSMA8	ENST00000343848.10	TSL:1	c.546+5141A>G		intron	N/A	ENSP00000345584.6

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

African (AFR) AF: 0.585 AC: 23685 AN: 40490

American (AMR) AF: 0.218 AC: 3307 AN: 15168

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 403 AN: 3454

East Asian (EAS) AF: 0.165 AC: 829 AN: 5026

South Asian (SAS) AF: 0.100 AC: 482 AN: 4804

European-Finnish (FIN) AF: 0.0927 AC: 961 AN: 10370

Middle Eastern (MID) AF: 0.110 AC: 32 AN: 292

European-Non Finnish (NFE) AF: 0.0709 AC: 4801 AN: 67710

Other (OTH) AF: 0.202 AC: 423 AN: 2098

Alfa AF: 0.124 Hom.: 3424

Bravo AF: 0.264

Asia WGS AF: 0.181 AC: 621 AN: 3446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.7
DANN	Benign	0.77
PhyloP100		-0.74
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11877878; hg19: chr18-23764235;