rs3758785
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_016540.4(GPR83):c.387+1888T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 152,120 control chromosomes in the GnomAD database, including 4,556 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 0.23 ( 4556 hom., cov: 32)
Consequence
GPR83
NM_016540.4 intron
NM_016540.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.559
Genes affected
GPR83 (HGNC:4523): (G protein-coupled receptor 83) Predicted to enable neuropeptide receptor activity. Predicted to be involved in neuropeptide signaling pathway. Predicted to act upstream of or within response to glucocorticoid. Located in cilium. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GPR83 | NM_016540.4 | c.387+1888T>C | intron_variant | ENST00000243673.7 | |||
GPR83 | NM_001330345.2 | c.387+1888T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPR83 | ENST00000243673.7 | c.387+1888T>C | intron_variant | 1 | NM_016540.4 | P1 | |||
GPR83 | ENST00000539203.2 | c.387+1888T>C | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.230 AC: 34891AN: 152002Hom.: 4558 Cov.: 32
GnomAD3 genomes
?
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152002
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.229 AC: 34908AN: 152120Hom.: 4556 Cov.: 32 AF XY: 0.229 AC XY: 17005AN XY: 74362
GnomAD4 genome
?
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34908
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152120
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32
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17005
AN XY:
74362
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Asia WGS
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AC:
784
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
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