rs2392510

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001381946.1(GPR141):​c.-15+21384C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.475 in 151,448 control chromosomes in the GnomAD database, including 17,268 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 0.47 ( 17268 hom., cov: 31)

Consequence

GPR141
NM_001381946.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.217
Variant links:
Genes affected
GPR141 (HGNC:19997): (G protein-coupled receptor 141) GPR141 is a member of the rhodopsin family of G protein-coupled receptors (GPRs) (Fredriksson et al., 2003 [PubMed 14623098]).[supplied by OMIM, Mar 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=-0.98).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.588 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
GPR141NM_001381946.1 linkuse as main transcriptc.-15+21384C>T intron_variant ENST00000334425.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
GPR141ENST00000334425.2 linkuse as main transcriptc.-15+21384C>T intron_variant NM_001381946.1 P1

Frequencies

GnomAD3 genomes
AF:
0.475
AC:
71830
AN:
151330
Hom.:
17257
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.479
Gnomad AMI
AF:
0.537
Gnomad AMR
AF:
0.518
Gnomad ASJ
AF:
0.431
Gnomad EAS
AF:
0.524
Gnomad SAS
AF:
0.607
Gnomad FIN
AF:
0.496
Gnomad MID
AF:
0.494
Gnomad NFE
AF:
0.447
Gnomad OTH
AF:
0.486
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.475
AC:
71867
AN:
151448
Hom.:
17268
Cov.:
31
AF XY:
0.481
AC XY:
35564
AN XY:
74012
show subpopulations
Gnomad4 AFR
AF:
0.479
Gnomad4 AMR
AF:
0.519
Gnomad4 ASJ
AF:
0.431
Gnomad4 EAS
AF:
0.523
Gnomad4 SAS
AF:
0.607
Gnomad4 FIN
AF:
0.496
Gnomad4 NFE
AF:
0.447
Gnomad4 OTH
AF:
0.481
Alfa
AF:
0.461
Hom.:
21545
Bravo
AF:
0.481
Asia WGS
AF:
0.546
AC:
1897
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
0.22
DANN
Benign
0.39

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2392510; hg19: chr7-37746569; API