rs10216533
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_005672.5(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
NM_005672.5 3_prime_UTR
NM_005672.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -3.78
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]
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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 | UniProt |
---|---|---|---|---|---|---|---|
PSCA | NM_005672.5 | c.*140G>A | 3_prime_UTR_variant | 3/3 | ENST00000301258.5 | ||
PSCA | NR_033343.2 | n.732G>A | non_coding_transcript_exon_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PSCA | ENST00000301258.5 | c.*140G>A | 3_prime_UTR_variant | 3/3 | 1 | NM_005672.5 | P1 | ||
PSCA | ENST00000510969.1 | n.708G>A | non_coding_transcript_exon_variant | 3/3 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.444 AC: 67307AN: 151690Hom.: 15073 Cov.: 32
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GnomAD3 exomes AF: 0.460 AC: 60509AN: 131454Hom.: 14284 AF XY: 0.456 AC XY: 32702AN XY: 71638
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GnomAD4 exome AF: 0.436 AC: 397052AN: 910296Hom.: 89003 Cov.: 12 AF XY: 0.438 AC XY: 204913AN XY: 467606
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GnomAD4 genome ? AF: 0.444 AC: 67375AN: 151808Hom.: 15100 Cov.: 32 AF XY: 0.445 AC XY: 32979AN XY: 74190
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at