Variant rs10216533 details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000301258.5(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
ENST00000301258.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.78

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=-0.93).

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	Protein	UniProt
PSCA	NM_005672.5 linkuse as main transcript	c.*140G>A		3_prime_UTR_variant	3/3	ENST00000301258.5	NP_005663.2
PSCA	NR_033343.2 linkuse as main transcript	n.732G>A		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PSCA	ENST00000301258.5 linkuse as main transcript	c.*140G>A		3_prime_UTR_variant	3/3	1	NM_005672.5	ENSP00000301258	P1
PSCA	ENST00000510969.1 linkuse as main transcript	n.708G>A		non_coding_transcript_exon_variant	3/3	2

Frequencies

GnomAD3 genomes

AF:

0.444

AC:

67307

AN:

151690

Hom.:

15073

Cov.:

show subpopulations

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

show subpopulations

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.:

AF XY:

0.438

AC XY:

204913

AN XY:

467606

show subpopulations

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.:

AF XY:

0.445

AC XY:

32979

AN XY:

74190

show subpopulations

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

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