rs11792431
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_004878.5(PTGES):c.45C>T(p.Ala15=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0671 in 1,610,762 control chromosomes in the GnomAD database, including 4,396 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 0.092 ( 893 hom., cov: 33)
Exomes 𝑓: 0.064 ( 3503 hom. )
Consequence
PTGES
NM_004878.5 synonymous
NM_004878.5 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.348
Genes affected
PTGES (HGNC:9599): (prostaglandin E synthase) The protein encoded by this gene is a glutathione-dependent prostaglandin E synthase. The expression of this gene has been shown to be induced by proinflammatory cytokine interleukin 1 beta (IL1B). Its expression can also be induced by tumor suppressor protein TP53, and may be involved in TP53 induced apoptosis. Knockout studies in mice suggest that this gene may contribute to the pathogenesis of collagen-induced arthritis and mediate acute pain during inflammatory responses. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.51).
BP7
?
Synonymous conserved (PhyloP=0.348 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.182 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTGES | NM_004878.5 | c.45C>T | p.Ala15= | synonymous_variant | 1/3 | ENST00000340607.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTGES | ENST00000340607.5 | c.45C>T | p.Ala15= | synonymous_variant | 1/3 | 1 | NM_004878.5 | P1 | |
PTGES | ENST00000481476.1 | n.52C>T | non_coding_transcript_exon_variant | 1/4 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0922 AC: 14039AN: 152202Hom.: 878 Cov.: 33
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GnomAD3 exomes AF: 0.0584 AC: 14454AN: 247448Hom.: 607 AF XY: 0.0575 AC XY: 7708AN XY: 134154
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GnomAD4 exome AF: 0.0645 AC: 94026AN: 1458442Hom.: 3503 Cov.: 32 AF XY: 0.0636 AC XY: 46150AN XY: 725686
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GnomAD4 genome ? AF: 0.0925 AC: 14084AN: 152320Hom.: 893 Cov.: 33 AF XY: 0.0905 AC XY: 6738AN XY: 74474
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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