1-70929000-T-C
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000370931.7(PTGER3):c.*23+24763A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.896 in 152,134 control chromosomes in the GnomAD database, including 61,271 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 0.90 ( 61271 hom., cov: 30)
Consequence
PTGER3
ENST00000370931.7 intron
ENST00000370931.7 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0720
Publications
7 publications found
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 was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.0).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.964 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PTGER3 | NM_198714.2 | c.*23+24763A>G | intron_variant | Intron 4 of 4 | NP_942007.1 | |||
PTGER3 | NM_198716.2 | c.1104+24763A>G | intron_variant | Intron 3 of 3 | NP_942009.1 | |||
PTGER3 | NM_198717.2 | c.1078-76141A>G | intron_variant | Intron 2 of 2 | NP_942010.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PTGER3 | ENST00000370931.7 | c.*23+24763A>G | intron_variant | Intron 4 of 4 | 1 | ENSP00000359969.3 | ||||
PTGER3 | ENST00000460330.5 | c.1104+24763A>G | intron_variant | Intron 3 of 3 | 1 | ENSP00000418073.1 | ||||
PTGER3 | ENST00000628037.2 | c.1078-76141A>G | intron_variant | Intron 2 of 2 | 1 | ENSP00000486617.1 |
Frequencies
GnomAD3 genomes AF: 0.896 AC: 136186AN: 152016Hom.: 61202 Cov.: 30 show subpopulations
GnomAD3 genomes
AF:
AC:
136186
AN:
152016
Hom.:
Cov.:
30
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.896 AC: 136315AN: 152134Hom.: 61271 Cov.: 30 AF XY: 0.898 AC XY: 66758AN XY: 74332 show subpopulations
GnomAD4 genome
AF:
AC:
136315
AN:
152134
Hom.:
Cov.:
30
AF XY:
AC XY:
66758
AN XY:
74332
show subpopulations
African (AFR)
AF:
AC:
40361
AN:
41542
American (AMR)
AF:
AC:
13864
AN:
15256
Ashkenazi Jewish (ASJ)
AF:
AC:
3001
AN:
3472
East Asian (EAS)
AF:
AC:
4799
AN:
5148
South Asian (SAS)
AF:
AC:
4134
AN:
4816
European-Finnish (FIN)
AF:
AC:
9336
AN:
10564
Middle Eastern (MID)
AF:
AC:
269
AN:
294
European-Non Finnish (NFE)
AF:
AC:
57841
AN:
68016
Other (OTH)
AF:
AC:
1913
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
711
1422
2133
2844
3555
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
900
1800
2700
3600
4500
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
3195
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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