rs1581688
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001146267.2(GPR85):c.*571A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.326 in 152,566 control chromosomes in the GnomAD database, including 8,478 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 0.33 ( 8454 hom., cov: 32)
Exomes 𝑓: 0.30 ( 24 hom. )
Consequence
GPR85
NM_001146267.2 3_prime_UTR
NM_001146267.2 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.456
Genes affected
GPR85 (HGNC:4536): (G protein-coupled receptor 85) Members of the G protein-coupled receptor (GPCR) family, such as GPR85, have a similar structure characterized by 7 transmembrane domains. Activation of GPCRs by extracellular stimuli, such as neurotransmitters, hormones, or light, induces an intracellular signaling cascade mediated by heterotrimeric GTP-binding proteins, or G proteins (Matsumoto et al., 2000 [PubMed 10833454]).[supplied by OMIM, Aug 2008]
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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=-0.52).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.38 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GPR85 | NM_001146267.2 | c.*571A>G | 3_prime_UTR_variant | 3/3 | ENST00000424100.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPR85 | ENST00000424100.2 | c.*571A>G | 3_prime_UTR_variant | 3/3 | 1 | NM_001146267.2 | P1 | ||
GPR85 | ENST00000297146.7 | c.*571A>G | 3_prime_UTR_variant | 3/3 | 1 | P1 | |||
GPR85 | ENST00000449591.2 | c.*571A>G | 3_prime_UTR_variant | 2/2 | 1 | P1 | |||
GPR85 | ENST00000610164.1 | c.*541+30A>G | intron_variant, NMD_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.327 AC: 49619AN: 151930Hom.: 8447 Cov.: 32
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GnomAD4 exome AF: 0.297 AC: 154AN: 518Hom.: 24 Cov.: 0 AF XY: 0.290 AC XY: 91AN XY: 314
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GnomAD4 genome ? AF: 0.327 AC: 49651AN: 152048Hom.: 8454 Cov.: 32 AF XY: 0.321 AC XY: 23884AN XY: 74312
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ClinVar
Not reported inComputational scores
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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