rs1045574

chr8-142682540-G-Achr8-142682540-G-Cchr8-142682540-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.*408G>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 0.455 in 445,148 control chromosomes in the GnomAD database, including 46,918 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 (14980 hom., cov: 32)
  • Exomes 𝑓: 0.46 (31938 hom.)
• Consequence: PSCA NM_005672.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

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=-0.9).
• 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.*408G>A		3_prime_UTR_variant	3/3	ENST00000301258.5
PSCA	NR_033343.2	n.1000G>A		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PSCA	ENST00000301258.5	c.*408G>A		3_prime_UTR_variant	3/3	1	NM_005672.5	P1

Frequencies

GnomAD3 genomes AF: 0.442 AC: 67063 AN: 151860 Hom.: 14953 Cov.: 32

Gnomad AFR AF: 0.388

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.511

Gnomad ASJ AF: 0.517

Gnomad EAS AF: 0.351

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.508

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.441

GnomAD3 exomes AF: 0.461 AC: 47412 AN: 102742 Hom.: 11157 AF XY: 0.459 AC XY: 25233 AN XY: 54982

Gnomad AFR exome AF: 0.376

Gnomad AMR exome AF: 0.560

Gnomad ASJ exome AF: 0.520

Gnomad EAS exome AF: 0.305

Gnomad SAS exome AF: 0.452

Gnomad FIN exome AF: 0.509

Gnomad NFE exome AF: 0.452

Gnomad OTH exome AF: 0.474

GnomAD4 exome AF: 0.462 AC: 135412 AN: 293168 Hom.: 31938 Cov.: 0 AF XY: 0.460 AC XY: 74782 AN XY: 162408

Gnomad4 AFR exome AF: 0.389

Gnomad4 AMR exome AF: 0.557

Gnomad4 ASJ exome AF: 0.508

Gnomad4 EAS exome AF: 0.381

Gnomad4 SAS exome AF: 0.454

Gnomad4 FIN exome AF: 0.505

Gnomad4 NFE exome AF: 0.453

Gnomad4 OTH exome AF: 0.462

GnomAD4 genome AF: 0.442 AC: 67129 AN: 151980 Hom.: 14980 Cov.: 32 AF XY: 0.442 AC XY: 32888 AN XY: 74340

Gnomad4 AFR AF: 0.389

Gnomad4 AMR AF: 0.511

Gnomad4 ASJ AF: 0.517

Gnomad4 EAS AF: 0.351

Gnomad4 SAS AF: 0.415

Gnomad4 FIN AF: 0.508

Gnomad4 NFE AF: 0.453

Gnomad4 OTH AF: 0.443

Alfa AF: 0.454 Hom.: 18910

Bravo AF: 0.439

Asia WGS AF: 0.407 AC: 1412 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	1.4
Dann	Benign	0.63

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: rs1045574; hg19: chr8-143763958; COSMIC: COSV56652338; COSMIC: COSV56652338;