rs11586015
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BS1BS2
The ENST00000374024.4(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
ENST00000374024.4 synonymous
ENST00000374024.4 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. Median coverage is 33. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 23 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GPR3 | NM_005281.4 | c.51C>A | p.Gly17= | 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.51C>A | p.Gly17= | synonymous_variant | 2/2 | 1 | NM_005281.4 | ENSP00000363136 | 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
Splicing
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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