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. Variant got -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

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

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.526

Gnomad4 AMR AF: 0.361

Gnomad4 ASJ AF: 0.387

Gnomad4 EAS AF: 0.197

Gnomad4 SAS AF: 0.159

Gnomad4 FIN AF: 0.292

Gnomad4 NFE AF: 0.365

Gnomad4 OTH AF: 0.387

Alfa AF: 0.355 Hom.: 6420

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2718058; hg19: chr7-37841534;