rs10216533

Variant names:

• chr8-142682272-G-A
• rs10216533
• NM_005672.5:c.*140G>A

Your query was ambiguous. Multiple possible variants found:

• chr8-142682272-G-A
• chr8-142682272-G-C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 28 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.503 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005672.5. 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.*140G>A		3_prime_UTR	Exon 3 of 3	NP_005663.2
	PSCA	NR_033343.2		n.732G>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.*140G>A		3_prime_UTR	Exon 3 of 3	ENSP00000301258.4
	PSCA	ENST00000510969.1	TSL:2	n.708G>A		non_coding_transcript_exon	Exon 3 of 3

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

GnomAD2 exomes AF: 0.460 AC: 60509 AN: 131454 AF XY: 0.456

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 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

African (AFR) AF: 0.376 AC: 8505 AN: 22646

American (AMR) AF: 0.551 AC: 19318 AN: 35080

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 11093 AN: 22168

East Asian (EAS) AF: 0.505 AC: 16986 AN: 33624

South Asian (SAS) AF: 0.448 AC: 31051 AN: 69324

European-Finnish (FIN) AF: 0.503 AC: 16771 AN: 33358

Middle Eastern (MID) AF: 0.484 AC: 2323 AN: 4804

European-Non Finnish (NFE) AF: 0.421 AC: 272464 AN: 646604

Other (OTH) AF: 0.434 AC: 18541 AN: 42688

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

African (AFR) AF: 0.397 AC: 16413 AN: 41364

American (AMR) AF: 0.512 AC: 7823 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.517 AC: 1792 AN: 3468

East Asian (EAS) AF: 0.351 AC: 1801 AN: 5130

South Asian (SAS) AF: 0.415 AC: 1999 AN: 4812

European-Finnish (FIN) AF: 0.507 AC: 5345 AN: 10544

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

European-Non Finnish (NFE) AF: 0.453 AC: 30771 AN: 67914

Other (OTH) AF: 0.446 AC: 938 AN: 2104

Alfa AF: 0.452 Hom.: 17570

Bravo AF: 0.441

Asia WGS AF: 0.403 AC: 1400 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.8
DANN	Benign	0.35
PhyloP100		-3.8
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: rs10216533; hg19: chr8-143763690; COSMIC: COSV56652313; COSMIC: COSV56652313;