Variant rs2976392 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_005672.5(PSCA):c.133+80G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.45 in 1,296,764 control chromosomes in the GnomAD database, including 134,274 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 0.45 ( 15416 hom., cov: 32)

Exomes 𝑓: 0.45 ( 118858 hom. )

Consequence

PSCA
NM_005672.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.38

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:

JRK (HGNC:6199): (Jrk helix-turn-helix protein) This gene encodes a conserved protein that is similar to DNA-binding proteins, such as major centromere autoantigen B (CENPB). Inactivation of the related gene in mice resulted in epileptic seizures. Childhood Absence Epilepsy (CAE) has been mapped to the same chromosomal location (8q24.3) as this gene. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]

JRK 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=-0.92).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.504 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PSCA	NM_005672.5 link	c.133+80G>A		intron_variant		ENST00000301258.5	NP_005663.2	O43653D3DWI6
PSCA	NR_033343.2 link	n.380+80G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PSCA	ENST00000301258.5 link	c.133+80G>A		intron_variant		1	NM_005672.5	ENSP00000301258.4		O43653

Frequencies

GnomAD3 genomes

AF:

0.449

AC:

68087

AN:

151782

Hom.:

15383

Cov.:

show subpopulations

Gnomad AFR

AF:

0.413

Gnomad AMI

AF:

0.391

Gnomad AMR

AF:

0.514

Gnomad ASJ

AF:

0.517

Gnomad EAS

AF:

0.353

Gnomad SAS

AF:

0.416

Gnomad FIN

AF:

0.507

Gnomad MID

AF:

0.484

Gnomad NFE

AF:

0.453

Gnomad OTH

AF:

0.447

GnomAD3 exomes

AF:

0.463

AC:

66033

AN:

142688

Hom.:

15620

AF XY:

0.460

AC XY:

35259

AN XY:

76684

show subpopulations

Gnomad AFR exome

AF:

0.402

Gnomad AMR exome

AF:

0.561

Gnomad ASJ exome

AF:

0.510

Gnomad EAS exome

AF:

0.303

Gnomad SAS exome

AF:

0.447

Gnomad FIN exome

AF:

0.510

Gnomad NFE exome

AF:

0.448

Gnomad OTH exome

AF:

0.473

GnomAD4 exome

AF:

0.450

AC:

514940

AN:

1144862

Hom.:

118858

Cov.:

AF XY:

0.450

AC XY:

258545

AN XY:

574178

show subpopulations

Gnomad4 AFR exome

AF:

0.402

Gnomad4 AMR exome

AF:

0.554

Gnomad4 ASJ exome

AF:

0.506

Gnomad4 EAS exome

AF:

0.502

Gnomad4 SAS exome

AF:

0.451

Gnomad4 FIN exome

AF:

0.504

Gnomad4 NFE exome

AF:

0.441

Gnomad4 OTH exome

AF:

0.443

GnomAD4 genome

AF:

0.449

AC:

68162

AN:

151902

Hom.:

15416

Cov.:

AF XY:

0.450

AC XY:

33385

AN XY:

74242

show subpopulations

Gnomad4 AFR

AF:

0.414

Gnomad4 AMR

AF:

0.514

Gnomad4 ASJ

AF:

0.517

Gnomad4 EAS

AF:

0.353

Gnomad4 SAS

AF:

0.415

Gnomad4 FIN

AF:

0.507

Gnomad4 NFE

AF:

0.453

Gnomad4 OTH

AF:

0.449

Alfa

AF:

0.452

Hom.:

12758

Bravo

AF:

0.447

Asia WGS

AF:

0.406

AC:

1408

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

1.2

DANN

Benign

0.50

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