rs2392510

chr7-37706967-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.217

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]

ACMG classification

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
GPR141	NM_001381946.1	c.-15+21384C>T		intron_variant		ENST00000334425.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GPR141	ENST00000334425.2	c.-15+21384C>T		intron_variant			NM_001381946.1	P1

Frequencies

GnomAD3 genomes AF: 0.475 AC: 71830 AN: 151330 Hom.: 17257 Cov.: 31

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

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

Other links and lift over

dbSNP: rs2392510; hg19: chr7-37746569;