chr2-218262686-C-T
Position:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_170699.3(GPBAR1):c.-39C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00481 in 1,506,832 control chromosomes in the GnomAD database, including 245 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 0.023 ( 111 hom., cov: 32)
Exomes 𝑓: 0.0028 ( 134 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: -1.88
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]
Genome browser will be placed here
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 = 0.0762 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GPBAR1 | NM_170699.3 | c.-39C>T | 5_prime_UTR_variant | 2/2 | ENST00000519574.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPBAR1 | ENST00000519574.2 | c.-39C>T | 5_prime_UTR_variant | 2/2 | 1 | NM_170699.3 | P1 | ||
GPBAR1 | ENST00000479077.5 | c.-39C>T | 5_prime_UTR_variant | 2/2 | 2 | P1 | |||
GPBAR1 | ENST00000521462.1 | c.-39C>T | 5_prime_UTR_variant | 2/2 | 2 | P1 | |||
GPBAR1 | ENST00000522678.5 | c.-39C>T | 5_prime_UTR_variant | 2/2 | 2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0231 AC: 3507AN: 152116Hom.: 110 Cov.: 32
GnomAD3 genomes
AF:
AC:
3507
AN:
152116
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.00656 AC: 963AN: 146828Hom.: 26 AF XY: 0.00532 AC XY: 419AN XY: 78708
GnomAD3 exomes
AF:
AC:
963
AN:
146828
Hom.:
AF XY:
AC XY:
419
AN XY:
78708
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00275 AC: 3727AN: 1354598Hom.: 134 Cov.: 30 AF XY: 0.00244 AC XY: 1618AN XY: 662960
GnomAD4 exome
AF:
AC:
3727
AN:
1354598
Hom.:
Cov.:
30
AF XY:
AC XY:
1618
AN XY:
662960
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.0231 AC: 3518AN: 152234Hom.: 111 Cov.: 32 AF XY: 0.0222 AC XY: 1654AN XY: 74428
GnomAD4 genome
AF:
AC:
3518
AN:
152234
Hom.:
Cov.:
32
AF XY:
AC XY:
1654
AN XY:
74428
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
20
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at