rs10216533

chr8-142682272-G-Achr8-142682272-G-C

Variant summary

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

The NM_005672.5(PSCA):c.*140G>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 0.437 in 1,062,104 control chromosomes in the GnomAD database, including 104,103 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 (15100 hom., cov: 32)
  • Exomes 𝑓: 0.44 (89003 hom.)
• Consequence: PSCA NM_005672.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.78

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.503 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PSCA	NM_005672.5	c.*140G>A		3_prime_UTR_variant	3/3	ENST00000301258.5
PSCA	NR_033343.2	n.732G>A		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PSCA	ENST00000301258.5	c.*140G>A		3_prime_UTR_variant	3/3	1	NM_005672.5	P1
PSCA	ENST00000510969.1	n.708G>A		non_coding_transcript_exon_variant	3/3	2

Frequencies

GnomAD3 genomes AF: 0.444 AC: 67307 AN: 151690 Hom.: 15073 Cov.: 32

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.517

Gnomad EAS AF: 0.351

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.444

GnomAD3 exomes AF: 0.460 AC: 60509 AN: 131454 Hom.: 14284 AF XY: 0.456 AC XY: 32702 AN XY: 71638

Gnomad AFR exome AF: 0.385

Gnomad AMR exome AF: 0.558

Gnomad ASJ exome AF: 0.509

Gnomad EAS exome AF: 0.302

Gnomad SAS exome AF: 0.447

Gnomad FIN exome AF: 0.506

Gnomad NFE exome AF: 0.447

Gnomad OTH exome AF: 0.474

GnomAD4 exome AF: 0.436 AC: 397052 AN: 910296 Hom.: 89003 Cov.: 12 AF XY: 0.438 AC XY: 204913 AN XY: 467606

Gnomad4 AFR exome AF: 0.376

Gnomad4 AMR exome AF: 0.551

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.505

Gnomad4 SAS exome AF: 0.448

Gnomad4 FIN exome AF: 0.503

Gnomad4 NFE exome AF: 0.421

Gnomad4 OTH exome AF: 0.434

GnomAD4 genome AF: 0.444 AC: 67375 AN: 151808 Hom.: 15100 Cov.: 32 AF XY: 0.445 AC XY: 32979 AN XY: 74190

Gnomad4 AFR AF: 0.397

Gnomad4 AMR AF: 0.512

Gnomad4 ASJ AF: 0.517

Gnomad4 EAS AF: 0.351

Gnomad4 SAS AF: 0.415

Gnomad4 FIN AF: 0.507

Gnomad4 NFE AF: 0.453

Gnomad4 OTH AF: 0.446

Alfa AF: 0.452 Hom.: 12463

Bravo AF: 0.441

Asia WGS AF: 0.403 AC: 1400 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	3.8
Dann	Benign	0.35

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: rs10216533; hg19: chr8-143763690; COSMIC: COSV56652313; COSMIC: COSV56652313;