12-56671929-C-T
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_006601.7(PTGES3):c.187-82G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.681 in 834,916 control chromosomes in the GnomAD database, including 194,710 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 0.70 ( 37276 hom., cov: 31)
Exomes 𝑓: 0.68 ( 157434 hom. )
Consequence
PTGES3
NM_006601.7 intron
NM_006601.7 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.27
Genes affected
PTGES3 (HGNC:16049): (prostaglandin E synthase 3) This gene encodes an enzyme that converts prostaglandin endoperoxide H2 (PGH2) to prostaglandin E2 (PGE2). This protein functions as a co-chaperone with heat shock protein 90 (HSP90), localizing to response elements in DNA and disrupting transcriptional activation complexes. Alternative splicing results in multiple transcript variants. There are multiple pseudogenes of this gene on several different chromosomes. [provided by RefSeq, Feb 2016]
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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 (SAS) allele frequency at 95% confidence interval = 0.771 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PTGES3 | NM_006601.7 | c.187-82G>A | intron_variant | ENST00000262033.11 | NP_006592.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PTGES3 | ENST00000262033.11 | c.187-82G>A | intron_variant | 1 | NM_006601.7 | ENSP00000262033.6 | ||||
PTGES3 | ENST00000456859.2 | c.117-120G>A | intron_variant | 2 | ENSP00000389090.2 |
Frequencies
GnomAD3 genomes AF: 0.699 AC: 106122AN: 151864Hom.: 37254 Cov.: 31
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GnomAD4 exome AF: 0.677 AC: 462351AN: 682934Hom.: 157434 AF XY: 0.679 AC XY: 232254AN XY: 342138
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GnomAD4 genome AF: 0.699 AC: 106197AN: 151982Hom.: 37276 Cov.: 31 AF XY: 0.703 AC XY: 52230AN XY: 74290
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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