rs2722292

Variant names:

• chr7-37784979-A-G
• rs2722292
• ENST00000476620.1:c.-109-72295A>G

Variant summary

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

The ENST00000476620.1(ENSG00000290149):​c.-109-72295A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 151,900 control chromosomes in the GnomAD database, including 3,014 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 0.18 (3014 hom., cov: 31)
• Consequence: ENSG00000290149 ENST00000476620.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.706
• Publications: 4 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=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.251 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000476620.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000290149	ENST00000476620.1	TSL:4	c.-109-72295A>G		intron	N/A	ENSP00000425858.1
	GPR141	ENST00000461610.5	TSL:1	n.233-44276A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27402 AN: 151782 Hom.: 3016 Cov.: 31

Gnomad AFR AF: 0.0538

Gnomad AMI AF: 0.228

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.180 AC: 27400 AN: 151900 Hom.: 3014 Cov.: 31 AF XY: 0.175 AC XY: 13013 AN XY: 74244

African (AFR) AF: 0.0536 AC: 2226 AN: 41500

American (AMR) AF: 0.218 AC: 3324 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.220 AC: 764 AN: 3466

East Asian (EAS) AF: 0.138 AC: 701 AN: 5088

South Asian (SAS) AF: 0.127 AC: 608 AN: 4806

European-Finnish (FIN) AF: 0.176 AC: 1861 AN: 10568

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.254 AC: 17233 AN: 67922

Other (OTH) AF: 0.193 AC: 407 AN: 2114

Alfa AF: 0.205 Hom.: 648

Bravo AF: 0.177

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.6
DANN	Benign	0.63
PhyloP100		-0.71
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: rs2722292; hg19: chr7-37824581;