rs5788
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1
The NM_000962.4(PTGS1):c.639C>A(p.Gly213Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 1,613,884 control chromosomes in the GnomAD database, including 27,432 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 0.27 ( 8808 hom., cov: 32)
Exomes 𝑓: 0.14 ( 18624 hom. )
Consequence
PTGS1
NM_000962.4 synonymous
NM_000962.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.377
Genes affected
PTGS1 (HGNC:9604): (prostaglandin-endoperoxide synthase 1) This is one of two genes encoding similar enzymes that catalyze the conversion of arachidonate to prostaglandin. The encoded protein regulates angiogenesis in endothelial cells, and is inhibited by nonsteroidal anti-inflammatory drugs such as aspirin. Based on its ability to function as both a cyclooxygenase and as a peroxidase, the encoded protein has been identified as a moonlighting protein. The protein may promote cell proliferation during tumor progression. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2021]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.35).
BP7
Synonymous conserved (PhyloP=-0.377 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.59 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PTGS1 | NM_000962.4 | c.639C>A | p.Gly213Gly | synonymous_variant | 6/11 | ENST00000362012.7 | NP_000953.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PTGS1 | ENST00000362012.7 | c.639C>A | p.Gly213Gly | synonymous_variant | 6/11 | 1 | NM_000962.4 | ENSP00000354612.2 |
Frequencies
GnomAD3 genomes AF: 0.267 AC: 40644AN: 151960Hom.: 8768 Cov.: 32
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GnomAD3 exomes AF: 0.165 AC: 41416AN: 251428Hom.: 5540 AF XY: 0.150 AC XY: 20423AN XY: 135882
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GnomAD4 exome AF: 0.137 AC: 200339AN: 1461806Hom.: 18624 Cov.: 33 AF XY: 0.135 AC XY: 97936AN XY: 727206
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GnomAD4 genome AF: 0.268 AC: 40741AN: 152078Hom.: 8808 Cov.: 32 AF XY: 0.263 AC XY: 19575AN XY: 74334
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Not reported inComputational scores
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Benign
CADD
Benign
DANN
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at