Variant chr8-142680513-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_005672.5(PSCA):c.-26C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.451 in 1,552,278 control chromosomes in the GnomAD database, including 159,752 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.45 ( 15469 hom., cov: 34)

Exomes 𝑓: 0.45 ( 144283 hom. )

Consequence

PSCA
NM_005672.5 5_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.133

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.62).

BP6

Variant 8-142680513-C-T is Benign according to our data. Variant chr8-142680513-C-T is described in ClinVar as [Benign]. Clinvar id is 704509.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

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	UniProt
PSCA	NM_005672.5 linkuse as main transcript	c.-26C>T		5_prime_UTR_variant	1/3	ENST00000301258.5
PSCA	NR_033343.2 linkuse as main transcript	n.273-814C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PSCA	ENST00000301258.5 linkuse as main transcript	c.-26C>T		5_prime_UTR_variant	1/3	1	NM_005672.5	P1

Frequencies

GnomAD3 genomes

AF:

0.449

AC:

68242

AN:

152088

Hom.:

15436

Cov.:

show subpopulations

Gnomad AFR

AF:

0.413

Gnomad AMI

AF:

0.389

Gnomad AMR

AF:

0.513

Gnomad ASJ

AF:

0.517

Gnomad EAS

AF:

0.352

Gnomad SAS

AF:

0.416

Gnomad FIN

AF:

0.507

Gnomad MID

AF:

0.481

Gnomad NFE

AF:

0.454

Gnomad OTH

AF:

0.447

GnomAD3 exomes

AF:

0.461

AC:

72528

AN:

157352

Hom.:

17061

AF XY:

0.458

AC XY:

38105

AN XY:

83284

show subpopulations

Gnomad AFR exome

AF:

0.401

Gnomad AMR exome

AF:

0.560

Gnomad ASJ exome

AF:

0.509

Gnomad EAS exome

AF:

0.303

Gnomad SAS exome

AF:

0.446

Gnomad FIN exome

AF:

0.507

Gnomad NFE exome

AF:

0.444

Gnomad OTH exome

AF:

0.472

GnomAD4 exome

AF:

0.451

AC:

631779

AN:

1400072

Hom.:

144283

Cov.:

AF XY:

0.452

AC XY:

311864

AN XY:

690692

show subpopulations

Gnomad4 AFR exome

AF:

0.402

Gnomad4 AMR exome

AF:

0.553

Gnomad4 ASJ exome

AF:

0.506

Gnomad4 EAS exome

AF:

0.496

Gnomad4 SAS exome

AF:

0.452

Gnomad4 FIN exome

AF:

0.505

Gnomad4 NFE exome

AF:

0.444

Gnomad4 OTH exome

AF:

0.444

GnomAD4 genome

AF:

0.449

AC:

68317

AN:

152206

Hom.:

15469

Cov.:

AF XY:

0.450

AC XY:

33458

AN XY:

74420

show subpopulations

Gnomad4 AFR

AF:

0.414

Gnomad4 AMR

AF:

0.514

Gnomad4 ASJ

AF:

0.517

Gnomad4 EAS

AF:

0.352

Gnomad4 SAS

AF:

0.416

Gnomad4 FIN

AF:

0.507

Gnomad4 NFE

AF:

0.454

Gnomad4 OTH

AF:

0.449

Alfa

AF:

0.451

Hom.:

35161

Bravo

AF:

0.447

Asia WGS

AF:

0.405

AC:

1407

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jul 02, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.62

CADD

Benign

DANN

Benign

0.76

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over