dbSNP rs2976396: PSCA:c.*451G>A (chr8-142682583-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0970

Variant links:

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]

PSCA links:

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ACMG classification

Classification made for transcript

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 rank	MANE	Protein	UniProt
PSCA	NM_005672.5 link	c.*451G>A		3_prime_UTR_variant	Exon 3 of 3	ENST00000301258.5	NP_005663.2	O43653D3DWI6
PSCA	NR_033343.2 link	n.1043G>A		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PSCA	ENST00000301258.5 link	c.*451G>A		3_prime_UTR_variant	Exon 3 of 3	1	NM_005672.5	ENSP00000301258.4		O43653

Frequencies

GnomAD3 genomes

AF:

0.441

AC:

67059

AN:

151936

Hom.:

14938

Cov.:

show subpopulations

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

show subpopulations

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.:

AF XY:

0.454

AC XY:

55263

AN XY:

121856

show subpopulations

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.:

AF XY:

0.442

AC XY:

32854

AN XY:

74326

show subpopulations

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over