rs2976396

chr8-142682583-G-Achr8-142682583-G-T

Variant summary

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

The NM_005672.5(PSCA):c.*451G>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 0.449 in 375,438 control chromosomes in the GnomAD database, including 38,492 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 0.44 (14965 hom., cov: 33)
  • Exomes 𝑓: 0.45 (23527 hom.)
• Consequence: PSCA NM_005672.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0970

Genes affected

PSCA (HGNC:9500): (prostate stem cell antigen) This gene encodes a glycosylphosphatidylinositol-anchored cell membrane glycoprotein. In addition to being highly expressed in the prostate it is also expressed in the bladder, placenta, colon, kidney, and stomach. This gene is up-regulated in a large proportion of prostate cancers and is also detected in cancers of the bladder and pancreas. This gene includes a polymorphism that results in an upstream start codon in some individuals; this polymorphism is thought to be associated with a risk for certain gastric and bladder cancers. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2010]

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 (AMR) allele frequency at 95% confidence interval = 0.502 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PSCA	NM_005672.5	c.*451G>A		3_prime_UTR_variant	3/3	ENST00000301258.5
PSCA	NR_033343.2	n.1043G>A		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PSCA	ENST00000301258.5	c.*451G>A		3_prime_UTR_variant	3/3	1	NM_005672.5	P1

Frequencies

GnomAD3 genomes AF: 0.441 AC: 67059 AN: 151936 Hom.: 14938 Cov.: 33

Gnomad AFR AF: 0.388

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.511

Gnomad ASJ AF: 0.517

Gnomad EAS AF: 0.352

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.442

GnomAD3 exomes AF: 0.447 AC: 30789 AN: 68864 Hom.: 6991 AF XY: 0.445 AC XY: 15754 AN XY: 35386

Gnomad AFR exome AF: 0.374

Gnomad AMR exome AF: 0.549

Gnomad ASJ exome AF: 0.511

Gnomad EAS exome AF: 0.312

Gnomad SAS exome AF: 0.441

Gnomad FIN exome AF: 0.503

Gnomad NFE exome AF: 0.447

Gnomad OTH exome AF: 0.451

GnomAD4 exome AF: 0.454 AC: 101512 AN: 223382 Hom.: 23527 Cov.: 0 AF XY: 0.454 AC XY: 55263 AN XY: 121856

Gnomad4 AFR exome AF: 0.381

Gnomad4 AMR exome AF: 0.546

Gnomad4 ASJ exome AF: 0.508

Gnomad4 EAS exome AF: 0.335

Gnomad4 SAS exome AF: 0.451

Gnomad4 FIN exome AF: 0.499

Gnomad4 NFE exome AF: 0.449

Gnomad4 OTH exome AF: 0.456

GnomAD4 genome AF: 0.441 AC: 67125 AN: 152056 Hom.: 14965 Cov.: 33 AF XY: 0.442 AC XY: 32854 AN XY: 74326

Gnomad4 AFR AF: 0.388

Gnomad4 AMR AF: 0.511

Gnomad4 ASJ AF: 0.517

Gnomad4 EAS AF: 0.352

Gnomad4 SAS AF: 0.415

Gnomad4 FIN AF: 0.507

Gnomad4 NFE AF: 0.453

Gnomad4 OTH AF: 0.444

Alfa AF: 0.455 Hom.: 12628

Bravo AF: 0.438

Asia WGS AF: 0.406 AC: 1411 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	4.6
Dann	Benign	0.41

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: rs2976396; hg19: chr8-143764001;