8-142681665-A-G
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_005672.5(PSCA):c.133+231A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.458 in 609,096 control chromosomes in the GnomAD database, including 65,065 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 ( 14944 hom., cov: 31)
Exomes 𝑓: 0.46 ( 50121 hom. )
Consequence
PSCA
NM_005672.5 intron
NM_005672.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -5.30
Publications
10 publications found
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]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.01).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.502 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.443 AC: 66953AN: 151304Hom.: 14917 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
66953
AN:
151304
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.464 AC: 212230AN: 457674Hom.: 50121 Cov.: 4 AF XY: 0.462 AC XY: 111310AN XY: 240714 show subpopulations
GnomAD4 exome
AF:
AC:
212230
AN:
457674
Hom.:
Cov.:
4
AF XY:
AC XY:
111310
AN XY:
240714
show subpopulations
African (AFR)
AF:
AC:
5013
AN:
12918
American (AMR)
AF:
AC:
11683
AN:
21578
Ashkenazi Jewish (ASJ)
AF:
AC:
7114
AN:
14068
East Asian (EAS)
AF:
AC:
16020
AN:
31034
South Asian (SAS)
AF:
AC:
21264
AN:
47410
European-Finnish (FIN)
AF:
AC:
15081
AN:
29922
Middle Eastern (MID)
AF:
AC:
1224
AN:
2556
European-Non Finnish (NFE)
AF:
AC:
122832
AN:
271784
Other (OTH)
AF:
AC:
11999
AN:
26404
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.495
Heterozygous variant carriers
0
5651
11302
16954
22605
28256
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
694
1388
2082
2776
3470
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome AF: 0.443 AC: 67019AN: 151422Hom.: 14944 Cov.: 31 AF XY: 0.443 AC XY: 32802AN XY: 73970 show subpopulations
GnomAD4 genome
AF:
AC:
67019
AN:
151422
Hom.:
Cov.:
31
AF XY:
AC XY:
32802
AN XY:
73970
show subpopulations
African (AFR)
AF:
AC:
16085
AN:
41206
American (AMR)
AF:
AC:
7794
AN:
15242
Ashkenazi Jewish (ASJ)
AF:
AC:
1790
AN:
3460
East Asian (EAS)
AF:
AC:
1800
AN:
5114
South Asian (SAS)
AF:
AC:
1985
AN:
4790
European-Finnish (FIN)
AF:
AC:
5356
AN:
10508
Middle Eastern (MID)
AF:
AC:
138
AN:
294
European-Non Finnish (NFE)
AF:
AC:
30787
AN:
67806
Other (OTH)
AF:
AC:
931
AN:
2096
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1913
3826
5738
7651
9564
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
622
1244
1866
2488
3110
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1397
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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