rs3736001
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1
The NM_005672.5(PSCA):c.88G>A(p.Glu30Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0198 in 1,593,088 control chromosomes in the GnomAD database, including 712 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_005672.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PSCA | NM_005672.5 | c.88G>A | p.Glu30Lys | missense_variant | 2/3 | ENST00000301258.5 | |
PSCA | NR_033343.2 | n.335G>A | non_coding_transcript_exon_variant | 2/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PSCA | ENST00000301258.5 | c.88G>A | p.Glu30Lys | missense_variant | 2/3 | 1 | NM_005672.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0156 AC: 2368AN: 152164Hom.: 59 Cov.: 33
GnomAD3 exomes AF: 0.0233 AC: 5002AN: 214314Hom.: 161 AF XY: 0.0250 AC XY: 2906AN XY: 116018
GnomAD4 exome AF: 0.0203 AC: 29195AN: 1440804Hom.: 653 Cov.: 32 AF XY: 0.0213 AC XY: 15254AN XY: 714500
GnomAD4 genome ? AF: 0.0156 AC: 2371AN: 152284Hom.: 59 Cov.: 33 AF XY: 0.0164 AC XY: 1220AN XY: 74454
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at