1-27394569-C-T
Position:
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BS1BS2
The NM_005281.4(GPR3):c.771C>T(p.Ala257Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.013 in 1,614,168 control chromosomes in the GnomAD database, including 185 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 0.0098 ( 15 hom., cov: 33)
Exomes 𝑓: 0.013 ( 170 hom. )
Consequence
GPR3
NM_005281.4 synonymous
NM_005281.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -4.68
Genes affected
GPR3 (HGNC:4484): (G protein-coupled receptor 3) This gene is a member of the G protein-coupled receptor family and is found in the cell membrane. G protein-coupled receptors, characterized by a seven transmembrane domain motif, are involved in translating outside signals into G protein mediated intracellular effects. The encoded protein activates adenylate cyclase and modulates amyloid-beta production in a mouse model, suggesting that it may play a role in Alzheimer's disease. [provided by RefSeq, Oct 2012]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.69).
BP7
Synonymous conserved (PhyloP=-4.68 with no splicing effect.
BS1
Variant frequency is greater than expected in population nfe. gnomad4_exome allele frequency = 0.0133 (19470/1461852) while in subpopulation NFE AF= 0.0154 (17142/1112000). AF 95% confidence interval is 0.0152. There are 170 homozygotes in gnomad4_exome. There are 9613 alleles in male gnomad4_exome subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 15 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GPR3 | NM_005281.4 | c.771C>T | p.Ala257Ala | synonymous_variant | 2/2 | ENST00000374024.4 | NP_005272.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GPR3 | ENST00000374024.4 | c.771C>T | p.Ala257Ala | synonymous_variant | 2/2 | 1 | NM_005281.4 | ENSP00000363136.3 |
Frequencies
GnomAD3 genomes AF: 0.00980 AC: 1491AN: 152198Hom.: 15 Cov.: 33
GnomAD3 genomes
AF:
AC:
1491
AN:
152198
Hom.:
Cov.:
33
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: 0.00968 AC: 2431AN: 251024Hom.: 14 AF XY: 0.00984 AC XY: 1335AN XY: 135674
GnomAD3 exomes
AF:
AC:
2431
AN:
251024
Hom.:
AF XY:
AC XY:
1335
AN XY:
135674
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: 0.0133 AC: 19470AN: 1461852Hom.: 170 Cov.: 32 AF XY: 0.0132 AC XY: 9613AN XY: 727230
GnomAD4 exome
AF:
AC:
19470
AN:
1461852
Hom.:
Cov.:
32
AF XY:
AC XY:
9613
AN XY:
727230
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: 0.00979 AC: 1491AN: 152316Hom.: 15 Cov.: 33 AF XY: 0.00943 AC XY: 702AN XY: 74482
GnomAD4 genome
AF:
AC:
1491
AN:
152316
Hom.:
Cov.:
33
AF XY:
AC XY:
702
AN XY:
74482
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:
7
AN:
3478
EpiCase
AF:
EpiControl
AF:
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