rs11586015
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BS1BS2
The NM_005281.4(GPR3):c.51C>A(p.Gly17=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0199 in 1,579,590 control chromosomes in the GnomAD database, including 400 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 0.014 ( 23 hom., cov: 33)
Exomes 𝑓: 0.021 ( 377 hom. )
Consequence
GPR3
NM_005281.4 synonymous
NM_005281.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0510
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.67).
BP7
?
Synonymous conserved (PhyloP=0.051 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.014 (2137/152310) while in subpopulation NFE AF= 0.0218 (1484/68012). AF 95% confidence interval is 0.0209. There are 23 homozygotes in gnomad4. There are 978 alleles in male gnomad4 subpopulation. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 23 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GPR3 | NM_005281.4 | c.51C>A | p.Gly17= | synonymous_variant | 2/2 | ENST00000374024.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPR3 | ENST00000374024.4 | c.51C>A | p.Gly17= | synonymous_variant | 2/2 | 1 | NM_005281.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0140 AC: 2136AN: 152192Hom.: 23 Cov.: 33
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GnomAD3 exomes AF: 0.0141 AC: 3275AN: 232144Hom.: 34 AF XY: 0.0147 AC XY: 1837AN XY: 125364
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GnomAD4 exome AF: 0.0205 AC: 29295AN: 1427280Hom.: 377 Cov.: 31 AF XY: 0.0198 AC XY: 13984AN XY: 705452
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GnomAD4 genome ? AF: 0.0140 AC: 2137AN: 152310Hom.: 23 Cov.: 33 AF XY: 0.0131 AC XY: 978AN XY: 74458
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at