rs5703
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The ENST00000370931.7(PTGER3):c.*24-9541T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00244 in 1,359,638 control chromosomes in the GnomAD database, including 74 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 0.012 ( 45 hom., cov: 32)
Exomes 𝑓: 0.0012 ( 29 hom. )
Consequence
PTGER3
ENST00000370931.7 intron
ENST00000370931.7 intron
Scores
2
Splicing: ADA: 0.00001375
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.13
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=-0.89).
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0125 (1899/152260) while in subpopulation AFR AF= 0.0434 (1804/41532). AF 95% confidence interval is 0.0418. There are 45 homozygotes in gnomad4. There are 910 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 45 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTGER3 | NM_198714.2 | c.*24-9541T>C | intron_variant | ||||
PTGER3 | NM_198716.2 | c.1105-9541T>C | intron_variant | ||||
PTGER3 | NM_198717.2 | c.1078-9541T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTGER3 | ENST00000370931.7 | c.*24-9541T>C | intron_variant | 1 | A1 | ||||
PTGER3 | ENST00000460330.5 | c.1105-9541T>C | intron_variant | 1 | A2 | ||||
PTGER3 | ENST00000628037.2 | c.1078-9541T>C | intron_variant | 1 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0125 AC: 1895AN: 152142Hom.: 45 Cov.: 32
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GnomAD3 exomes AF: 0.00313 AC: 777AN: 248474Hom.: 17 AF XY: 0.00219 AC XY: 295AN XY: 134498
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GnomAD4 exome AF: 0.00117 AC: 1415AN: 1207378Hom.: 29 Cov.: 27 AF XY: 0.000930 AC XY: 557AN XY: 598882
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GnomAD4 genome ? AF: 0.0125 AC: 1899AN: 152260Hom.: 45 Cov.: 32 AF XY: 0.0122 AC XY: 910AN XY: 74460
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ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
Find out detailed SpliceAI scores and Pangolin per-transcript scores at