rs12702047
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001098201.3(GPER1):c.*228G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 684,992 control chromosomes in the GnomAD database, including 9,595 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 0.15 ( 1854 hom., cov: 32)
Exomes 𝑓: 0.17 ( 7741 hom. )
Consequence
GPER1
NM_001098201.3 3_prime_UTR
NM_001098201.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.04
Genes affected
GPER1 (HGNC:4485): (G protein-coupled estrogen receptor 1) This gene encodes a multi-pass membrane protein that localizes to the endoplasmic reticulum and a member of the G-protein coupled receptor 1 family. This receptor binds estrogen and activates multiple downstream signaling pathways, leading to stimulation of adenylate cyclase and an increase in cyclic AMP levels, while also promoting intracellular calcium mobilization and synthesis of phosphatidylinositol 3,4,5-trisphosphate in the nucleus. This protein therefore plays a role in the rapid nongenomic signaling events widely observed following stimulation of cells and tissues with estrogen. This receptor has been shown to play a role in diverse biological processes, including bone and nervous system development, metabolism, cognition, male fertility and uterine function. [provided by RefSeq, Aug 2017]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.168 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GPER1 | NM_001098201.3 | c.*228G>A | 3_prime_UTR_variant | 2/2 | ENST00000397088.4 | ||
C7orf50 | NM_001318252.2 | c.129+34173C>T | intron_variant | ENST00000397098.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPER1 | ENST00000397088.4 | c.*228G>A | 3_prime_UTR_variant | 2/2 | 1 | NM_001098201.3 | P1 | ||
C7orf50 | ENST00000397098.8 | c.129+34173C>T | intron_variant | 1 | NM_001318252.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.147 AC: 22412AN: 151950Hom.: 1849 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
22412
AN:
151950
Hom.:
Cov.:
32
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:
GnomAD3 exomes AF: 0.167 AC: 24573AN: 146768Hom.: 2238 AF XY: 0.167 AC XY: 13248AN XY: 79236
GnomAD3 exomes
AF:
AC:
24573
AN:
146768
Hom.:
AF XY:
AC XY:
13248
AN XY:
79236
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.165 AC: 87938AN: 532924Hom.: 7741 Cov.: 3 AF XY: 0.165 AC XY: 47542AN XY: 288400
GnomAD4 exome
AF:
AC:
87938
AN:
532924
Hom.:
Cov.:
3
AF XY:
AC XY:
47542
AN XY:
288400
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.147 AC: 22430AN: 152068Hom.: 1854 Cov.: 32 AF XY: 0.147 AC XY: 10930AN XY: 74338
GnomAD4 genome
?
AF:
AC:
22430
AN:
152068
Hom.:
Cov.:
32
AF XY:
AC XY:
10930
AN XY:
74338
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
429
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at