rs2302821
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004878.5(PTGES):c.*9T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 1,548,682 control chromosomes in the GnomAD database, including 20,091 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 0.19 ( 4119 hom., cov: 32)
Exomes 𝑓: 0.11 ( 15972 hom. )
Consequence
PTGES
NM_004878.5 3_prime_UTR
NM_004878.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.70
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTGES | NM_004878.5 | c.*9T>G | 3_prime_UTR_variant | 3/3 | ENST00000340607.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTGES | ENST00000340607.5 | c.*9T>G | 3_prime_UTR_variant | 3/3 | 1 | NM_004878.5 | P1 | ||
PTGES | ENST00000481476.1 | n.597T>G | non_coding_transcript_exon_variant | 4/4 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.187 AC: 28369AN: 152042Hom.: 4110 Cov.: 32
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GnomAD3 exomes AF: 0.171 AC: 26438AN: 154458Hom.: 3843 AF XY: 0.171 AC XY: 13963AN XY: 81496
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GnomAD4 exome AF: 0.112 AC: 157055AN: 1396522Hom.: 15972 Cov.: 31 AF XY: 0.115 AC XY: 79199AN XY: 688608
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GnomAD4 genome ? AF: 0.187 AC: 28413AN: 152160Hom.: 4119 Cov.: 32 AF XY: 0.191 AC XY: 14216AN XY: 74390
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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