rs56192869
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_170699.3(GPBAR1):c.-31G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00517 in 1,520,630 control chromosomes in the GnomAD database, including 297 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 0.025 ( 138 hom., cov: 32)
Exomes 𝑓: 0.0029 ( 159 hom. )
Consequence
GPBAR1
NM_170699.3 5_prime_UTR
NM_170699.3 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.458
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 Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0834 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GPBAR1 | NM_170699.3 | c.-31G>A | 5_prime_UTR_variant | 2/2 | ENST00000519574.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPBAR1 | ENST00000519574.2 | c.-31G>A | 5_prime_UTR_variant | 2/2 | 1 | NM_170699.3 | P1 | ||
GPBAR1 | ENST00000479077.5 | c.-31G>A | 5_prime_UTR_variant | 2/2 | 2 | P1 | |||
GPBAR1 | ENST00000521462.1 | c.-31G>A | 5_prime_UTR_variant | 2/2 | 2 | P1 | |||
GPBAR1 | ENST00000522678.5 | c.-31G>A | 5_prime_UTR_variant | 2/2 | 2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0252 AC: 3829AN: 151980Hom.: 138 Cov.: 32
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GnomAD3 exomes AF: 0.00705 AC: 1163AN: 165018Hom.: 44 AF XY: 0.00563 AC XY: 503AN XY: 89346
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GnomAD4 exome AF: 0.00294 AC: 4024AN: 1368532Hom.: 159 Cov.: 31 AF XY: 0.00262 AC XY: 1761AN XY: 671276
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GnomAD4 genome ? AF: 0.0252 AC: 3840AN: 152098Hom.: 138 Cov.: 32 AF XY: 0.0241 AC XY: 1793AN XY: 74352
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ClinVar
Not reported inComputational scores
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Name
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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