rs17482481
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000370931.7(PTGER3):c.*23+50080A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 151,874 control chromosomes in the GnomAD database, including 6,973 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 0.30 ( 6973 hom., cov: 32)
Consequence
PTGER3
ENST00000370931.7 intron
ENST00000370931.7 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.213
Genes affected
PTGER3 (HGNC:9595): (prostaglandin E receptor 3) The protein encoded by this gene is a member of the G-protein coupled receptor family. This protein is one of four receptors identified for prostaglandin E2 (PGE2). This receptor may have many biological functions, which involve digestion, nervous system, kidney reabsorption, and uterine contraction activities. Studies of the mouse counterpart suggest that this receptor may also mediate adrenocorticotropic hormone response as well as fever generation in response to exogenous and endogenous stimuli. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2009]
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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=-0.99).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.438 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTGER3 | NM_198714.2 | c.*23+50080A>C | intron_variant | ||||
PTGER3 | NM_198716.2 | c.1104+50080A>C | intron_variant | ||||
PTGER3 | NM_198717.2 | c.1078-50824A>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTGER3 | ENST00000370931.7 | c.*23+50080A>C | intron_variant | 1 | A1 | ||||
PTGER3 | ENST00000460330.5 | c.1104+50080A>C | intron_variant | 1 | A2 | ||||
PTGER3 | ENST00000628037.2 | c.1078-50824A>C | intron_variant | 1 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.297 AC: 45074AN: 151758Hom.: 6960 Cov.: 32
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.297 AC: 45129AN: 151874Hom.: 6973 Cov.: 32 AF XY: 0.304 AC XY: 22550AN XY: 74212
GnomAD4 genome
?
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32
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22550
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1487
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3476
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at