rs2392510

Variant names:

• chr7-37706967-C-T
• rs2392510
• NM_001381946.1:c.-15+21384C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 13 publications found

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]

ENSG00000290149 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001381946.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GPR141	NM_001381946.1	MANE Select	c.-15+21384C>T		intron	N/A	NP_001368875.1	Q7Z602
	GPR141	NM_001329993.2		c.-138+21384C>T		intron	N/A	NP_001316922.1	Q7Z602
	GPR141	NM_001329994.2		c.-15+21384C>T		intron	N/A	NP_001316923.1	Q7Z602

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GPR141	ENST00000334425.2	TSL:6 MANE Select	c.-15+21384C>T		intron	N/A	ENSP00000334540.1	Q7Z602
	ENSG00000290149	ENST00000476620.1	TSL:4	c.-110+23064C>T		intron	N/A	ENSP00000425858.1	D6RIH7
	GPR141	ENST00000461610.5	TSL:1	n.232+21384C>T		intron	N/A

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

African (AFR) AF: 0.479 AC: 19745 AN: 41250

American (AMR) AF: 0.519 AC: 7896 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.431 AC: 1494 AN: 3468

East Asian (EAS) AF: 0.523 AC: 2677 AN: 5122

South Asian (SAS) AF: 0.607 AC: 2913 AN: 4800

European-Finnish (FIN) AF: 0.496 AC: 5210 AN: 10498

Middle Eastern (MID) AF: 0.483 AC: 140 AN: 290

European-Non Finnish (NFE) AF: 0.447 AC: 30292 AN: 67790

Other (OTH) AF: 0.481 AC: 1012 AN: 2102

Alfa AF: 0.464 Hom.: 27542

Bravo AF: 0.481

Asia WGS AF: 0.546 AC: 1897 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.22
DANN	Benign	0.39
PhyloP100		-0.22
Mutation Taster		=100/0	polymorphism (auto)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2392510; hg19: chr7-37746569;