2-218262736-C-T
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Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6BP7
The NM_170699.3(GPBAR1):c.12C>T(p.Asn4=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000156 in 1,591,254 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Genomes: 𝑓 0.00016 ( 1 hom., cov: 32)
Exomes 𝑓: 0.00015 ( 1 hom. )
Consequence
GPBAR1
NM_170699.3 synonymous
NM_170699.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.03
Genes affected
GPBAR1 (HGNC:19680): (G protein-coupled bile acid receptor 1) This gene encodes a member of the G protein-coupled receptor (GPCR) superfamily. This enzyme functions as a cell surface receptor for bile acids. Treatment of cells expressing this GPCR with bile acids induces the production of intracellular cAMP, activation of a MAP kinase signaling pathway, and internalization of the receptor. The receptor is implicated in the suppression of macrophage functions and regulation of energy homeostasis by bile acids. Alternative splicing results in multiple transcript variants encoding the same protein. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.63).
BP6
Variant 2-218262736-C-T is Benign according to our data. Variant chr2-218262736-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3358501.Status of the report is no_assertion_criteria_provided, 0 stars.
BP7
Synonymous conserved (PhyloP=1.03 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GPBAR1 | NM_170699.3 | c.12C>T | p.Asn4= | synonymous_variant | 2/2 | ENST00000519574.2 | NP_733800.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GPBAR1 | ENST00000519574.2 | c.12C>T | p.Asn4= | synonymous_variant | 2/2 | 1 | NM_170699.3 | ENSP00000430202 | P1 | |
GPBAR1 | ENST00000479077.5 | c.12C>T | p.Asn4= | synonymous_variant | 2/2 | 2 | ENSP00000430698 | P1 | ||
GPBAR1 | ENST00000521462.1 | c.12C>T | p.Asn4= | synonymous_variant | 2/2 | 2 | ENSP00000428824 | P1 | ||
GPBAR1 | ENST00000522678.5 | c.12C>T | p.Asn4= | synonymous_variant | 2/2 | 2 | ENSP00000430886 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000164 AC: 25AN: 152128Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.000277 AC: 64AN: 231264Hom.: 1 AF XY: 0.000222 AC XY: 28AN XY: 126306
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GnomAD4 exome AF: 0.000155 AC: 223AN: 1439126Hom.: 1 Cov.: 31 AF XY: 0.000160 AC XY: 114AN XY: 712916
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GnomAD4 genome AF: 0.000164 AC: 25AN: 152128Hom.: 1 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74296
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
GPBAR1-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 23, 2024 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Benign
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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