rs2718058

Variant names:

• chr7-37801932-A-G
• rs2718058
• ENST00000476620.1:c.-109-55342A>G

Your query was ambiguous. Multiple possible variants found:

• chr7-37801932-A-G
• chr7-37801932-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000476620.1(ENSG00000290149):​c.-109-55342A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.391 in 151,128 control chromosomes in the GnomAD database, including 12,231 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 0.39 (12231 hom., cov: 31)
• Consequence: ENSG00000290149 ENST00000476620.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.863
• Publications: 104 publications found

Genes affected

ENSG00000290149 (HGNC:):

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.52 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000290149	ENST00000476620.1	c.-109-55342A>G		intron_variant	Intron 1 of 3	4		ENSP00000425858.1
GPR141	ENST00000461610.5	n.233-27323A>G		intron_variant	Intron 2 of 3	1

Frequencies

GnomAD3 genomes AF: 0.391 AC: 59108 AN: 151012 Hom.: 12219 Cov.: 31

Gnomad AFR AF: 0.526

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.387

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.397

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.388

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.391 AC: 59166 AN: 151128 Hom.: 12231 Cov.: 31 AF XY: 0.382 AC XY: 28207 AN XY: 73786

African (AFR) AF: 0.526 AC: 21684 AN: 41220

American (AMR) AF: 0.361 AC: 5492 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.387 AC: 1343 AN: 3466

East Asian (EAS) AF: 0.197 AC: 1010 AN: 5114

South Asian (SAS) AF: 0.159 AC: 760 AN: 4786

European-Finnish (FIN) AF: 0.292 AC: 3023 AN: 10360

Middle Eastern (MID) AF: 0.417 AC: 120 AN: 288

European-Non Finnish (NFE) AF: 0.365 AC: 24685 AN: 67670

Other (OTH) AF: 0.387 AC: 814 AN: 2106

Alfa AF: 0.370 Hom.: 24555

Bravo AF: 0.401

Asia WGS AF: 0.208 AC: 726 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.99
DANN	Benign	0.57
PhyloP100		-0.86
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs2718058; hg19: chr7-37841534;