chr10-25176269-T-C
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_ModerateBP6_ModerateBP7
The NM_020752.3(GPR158):c.849T>C(p.Val283=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000288 in 1,610,002 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00039 ( 1 hom., cov: 33)
Exomes 𝑓: 0.00028 ( 2 hom. )
Consequence
GPR158
NM_020752.3 synonymous
NM_020752.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0450
Genes affected
GPR158 (HGNC:23689): (G protein-coupled receptor 158) Predicted to enable G protein-coupled receptor activity. Predicted to act upstream of or within G protein-coupled receptor signaling pathway and protein localization to plasma membrane. Predicted to be located in membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.4).
BP6
?
Variant 10-25176269-T-C is Benign according to our data. Variant chr10-25176269-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 2640360.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.045 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GPR158 | NM_020752.3 | c.849T>C | p.Val283= | synonymous_variant | 1/11 | ENST00000376351.4 | |
GPR158-AS1 | NR_027333.2 | n.8A>G | non_coding_transcript_exon_variant | 1/2 | |||
GPR158 | XR_930512.4 | n.1269T>C | non_coding_transcript_exon_variant | 1/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPR158 | ENST00000376351.4 | c.849T>C | p.Val283= | synonymous_variant | 1/11 | 1 | NM_020752.3 | P2 | |
GPR158-AS1 | ENST00000449643.1 | n.8A>G | non_coding_transcript_exon_variant | 1/2 | 2 | ||||
GPR158 | ENST00000650135.1 | c.612T>C | p.Val204= | synonymous_variant | 2/12 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.000388 AC: 59AN: 152176Hom.: 1 Cov.: 33
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GnomAD3 exomes AF: 0.000809 AC: 196AN: 242412Hom.: 0 AF XY: 0.000780 AC XY: 102AN XY: 130712
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GnomAD4 exome AF: 0.000277 AC: 404AN: 1457708Hom.: 2 Cov.: 32 AF XY: 0.000290 AC XY: 210AN XY: 724626
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Oct 01, 2022 | GPR158: BP4, BP7 - |
Computational scores
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BayesDel_noAF
Benign
Cadd
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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