rs1045574

Variant names:

• chr8-142682540-G-A
• rs1045574
• NM_005672.5:c.*408G>A

Your query was ambiguous. Multiple possible variants found:

• chr8-142682540-G-A
• chr8-142682540-G-C
• chr8-142682540-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000301258.5(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 ENST00000301258.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 21 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000301258.5. 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
	PSCA	NM_005672.5	MANE Select	c.*408G>A		3_prime_UTR	Exon 3 of 3	NP_005663.2
	PSCA	NR_033343.2		n.1000G>A		non_coding_transcript_exon	Exon 3 of 3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PSCA	ENST00000301258.5	TSL:1 MANE Select	c.*408G>A		3_prime_UTR	Exon 3 of 3	ENSP00000301258.4
	PSCA	ENST00000510969.1	TSL:2	n.*241G>A		downstream_gene	N/A

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

GnomAD2 exomes AF: 0.461 AC: 47412 AN: 102742 AF XY: 0.459

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 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

African (AFR) AF: 0.389 AC: 3478 AN: 8944

American (AMR) AF: 0.557 AC: 13682 AN: 24582

Ashkenazi Jewish (ASJ) AF: 0.508 AC: 4659 AN: 9172

East Asian (EAS) AF: 0.381 AC: 4115 AN: 10796

South Asian (SAS) AF: 0.454 AC: 24334 AN: 53602

European-Finnish (FIN) AF: 0.505 AC: 6474 AN: 12814

Middle Eastern (MID) AF: 0.493 AC: 1365 AN: 2770

European-Non Finnish (NFE) AF: 0.453 AC: 70656 AN: 156098

Other (OTH) AF: 0.462 AC: 6649 AN: 14390

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

African (AFR) AF: 0.389 AC: 16112 AN: 41430

American (AMR) AF: 0.511 AC: 7816 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.517 AC: 1795 AN: 3472

East Asian (EAS) AF: 0.351 AC: 1804 AN: 5142

South Asian (SAS) AF: 0.415 AC: 1996 AN: 4812

European-Finnish (FIN) AF: 0.508 AC: 5376 AN: 10588

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.453 AC: 30803 AN: 67938

Other (OTH) AF: 0.443 AC: 934 AN: 2108

Alfa AF: 0.452 Hom.: 22837

Bravo AF: 0.439

Asia WGS AF: 0.407 AC: 1412 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.63
PhyloP100		-1.0
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: rs1045574; hg19: chr8-143763958; COSMIC: COSV56652338; COSMIC: COSV56652338;