ENST00000476620.1:c.-109-72295A>G

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.251 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.-109-72295A>G		intron_variant	Intron 1 of 3	4		ENSP00000425858.1
GPR141	ENST00000461610.5	n.233-44276A>G		intron_variant	Intron 2 of 3	1

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

Gnomad4 AFR AF: 0.0536

Gnomad4 AMR AF: 0.218

Gnomad4 ASJ AF: 0.220

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.127

Gnomad4 FIN AF: 0.176

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.193

Alfa AF: 0.209 Hom.: 646

Bravo AF: 0.177

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.6
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2722292; hg19: chr7-37824581;