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GeneBe

rs2294008

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

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

2

Clinical Significance

Benign criteria provided, single submitter B:1

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]
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 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_single_submitter, 1 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
PSCANM_005672.5 linkuse as main transcriptc.-26C>T 5_prime_UTR_variant 1/3 ENST00000301258.5
PSCANR_033343.2 linkuse as main transcriptn.273-814C>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PSCAENST00000301258.5 linkuse as main transcriptc.-26C>T 5_prime_UTR_variant 1/31 NM_005672.5 P1

Frequencies

GnomAD3 genomes
AF:
0.449
AC:
68242
AN:
152088
Hom.:
15436
Cov.:
34
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.:
45
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.:
34
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:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeJul 02, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.62
Cadd
Benign
12
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.

Other links and lift over

dbSNP: rs2294008; hg19: chr8-143761931; COSMIC: COSV56652380; API