rs2718051

Positions:

• chr7-37785188-G-A
• chr7-37785188-G-T

Variant summary

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

The ENST00000461610.5(GPR141):​n.233-44067G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 152,048 control chromosomes in the GnomAD database, including 3,084 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 0.19 (3084 hom., cov: 31)
• Consequence: GPR141 ENST00000461610.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.894

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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GPR141	ENST00000461610.5	n.233-44067G>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28331 AN: 151928 Hom.: 3086 Cov.: 31

Gnomad AFR AF: 0.0753

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.186 AC: 28337 AN: 152048 Hom.: 3084 Cov.: 31 AF XY: 0.181 AC XY: 13481 AN XY: 74314

Gnomad4 AFR AF: 0.0753

Gnomad4 AMR AF: 0.220

Gnomad4 ASJ AF: 0.220

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.127

Gnomad4 FIN AF: 0.176

Gnomad4 NFE AF: 0.253

Gnomad4 OTH AF: 0.196

Alfa AF: 0.225 Hom.: 1944

Bravo AF: 0.184

Asia WGS AF: 0.130 AC: 454 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.38
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2718051; hg19: chr7-37824790;