1-70929000-T-C

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0720

Publications

7 publications found
Variant links:
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]

Genome browser will be placed here

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
PTGER3NM_198714.2 linkc.*23+24763A>G intron_variant Intron 4 of 4 NP_942007.1 P43115-1
PTGER3NM_198716.2 linkc.1104+24763A>G intron_variant Intron 3 of 3 NP_942009.1 P43115-4
PTGER3NM_198717.2 linkc.1078-76141A>G intron_variant Intron 2 of 2 NP_942010.1 P43115-3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PTGER3ENST00000370931.7 linkc.*23+24763A>G intron_variant Intron 4 of 4 1 ENSP00000359969.3 P43115-1
PTGER3ENST00000460330.5 linkc.1104+24763A>G intron_variant Intron 3 of 3 1 ENSP00000418073.1 P43115-4
PTGER3ENST00000628037.2 linkc.1078-76141A>G intron_variant Intron 2 of 2 1 ENSP00000486617.1 P43115-3

Frequencies

GnomAD3 genomes
AF:
0.896
AC:
136186
AN:
152016
Hom.:
61202
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.971
Gnomad AMI
AF:
0.874
Gnomad AMR
AF:
0.909
Gnomad ASJ
AF:
0.864
Gnomad EAS
AF:
0.932
Gnomad SAS
AF:
0.857
Gnomad FIN
AF:
0.884
Gnomad MID
AF:
0.918
Gnomad NFE
AF:
0.850
Gnomad OTH
AF:
0.904
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.896
AC:
136315
AN:
152134
Hom.:
61271
Cov.:
30
AF XY:
0.898
AC XY:
66758
AN XY:
74332
show subpopulations
African (AFR)
AF:
0.972
AC:
40361
AN:
41542
American (AMR)
AF:
0.909
AC:
13864
AN:
15256
Ashkenazi Jewish (ASJ)
AF:
0.864
AC:
3001
AN:
3472
East Asian (EAS)
AF:
0.932
AC:
4799
AN:
5148
South Asian (SAS)
AF:
0.858
AC:
4134
AN:
4816
European-Finnish (FIN)
AF:
0.884
AC:
9336
AN:
10564
Middle Eastern (MID)
AF:
0.915
AC:
269
AN:
294
European-Non Finnish (NFE)
AF:
0.850
AC:
57841
AN:
68016
Other (OTH)
AF:
0.905
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:
0.866
Hom.:
123950
Bravo
AF:
0.902
Asia WGS
AF:
0.919
AC:
3195
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
6.7
DANN
Benign
0.36
PhyloP100
0.072
Mutation Taster
=100/0
polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs578096; hg19: chr1-71394683; API