7-113083393-C-T
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The ENST00000424100.2(GPR85):c.*216G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0141 in 539,658 control chromosomes in the GnomAD database, including 77 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 0.012 ( 21 hom., cov: 32)
Exomes 𝑓: 0.015 ( 56 hom. )
Consequence
GPR85
ENST00000424100.2 3_prime_UTR
ENST00000424100.2 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.29
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=-0.57).
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0123 (1880/152254) while in subpopulation NFE AF= 0.0203 (1379/68024). AF 95% confidence interval is 0.0194. There are 21 homozygotes in gnomad4. There are 849 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 21 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GPR85 | NM_001146267.2 | c.*216G>A | 3_prime_UTR_variant | 3/3 | ENST00000424100.2 | NP_001139739.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GPR85 | ENST00000424100.2 | c.*216G>A | 3_prime_UTR_variant | 3/3 | 1 | NM_001146267.2 | ENSP00000396763 | P1 | ||
GPR85 | ENST00000297146.7 | c.*216G>A | 3_prime_UTR_variant | 3/3 | 1 | ENSP00000297146 | P1 | |||
GPR85 | ENST00000449591.2 | c.*216G>A | 3_prime_UTR_variant | 2/2 | 1 | ENSP00000401178 | P1 | |||
GPR85 | ENST00000610164.1 | c.*216G>A | 3_prime_UTR_variant, NMD_transcript_variant | 2/3 | 5 | ENSP00000476863 |
Frequencies
GnomAD3 genomes AF: 0.0123 AC: 1878AN: 152138Hom.: 21 Cov.: 32
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GnomAD4 exome AF: 0.0148 AC: 5739AN: 387404Hom.: 56 Cov.: 4 AF XY: 0.0149 AC XY: 3013AN XY: 201988
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GnomAD4 genome AF: 0.0123 AC: 1880AN: 152254Hom.: 21 Cov.: 32 AF XY: 0.0114 AC XY: 849AN XY: 74432
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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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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at