rs746408116
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PM4
The NM_000929.3(PLA2G5):c.185G>A(p.Trp62Ter) variant causes a stop gained, splice region change. The variant allele was found at a frequency of 0.00000684 in 1,461,782 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 2/2 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Affects (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_000929.3 stop_gained, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLA2G5 | NM_000929.3 | c.185G>A | p.Trp62Ter | stop_gained, splice_region_variant | 3/5 | ENST00000375108.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLA2G5 | ENST00000375108.4 | c.185G>A | p.Trp62Ter | stop_gained, splice_region_variant | 3/5 | 1 | NM_000929.3 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251130Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135722
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461782Hom.: 0 Cov.: 31 AF XY: 0.0000110 AC XY: 8AN XY: 727202
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Familial benign flecked retina Other:1
Affects, no assertion criteria provided | literature only | OMIM | Dec 09, 2011 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at