ENST00000476620.1:c.-110+67390A>G

Variant names:

• chr7-37751293-A-G
• rs2709114
• ENST00000476620.1:c.-110+67390A>G

Variant summary

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

The ENST00000476620.1(ENSG00000290149):​c.-110+67390A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.847 in 151,726 control chromosomes in the GnomAD database, including 54,486 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 0.85 (54486 hom., cov: 28)
• Consequence: ENSG00000290149 ENST00000476620.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.690
• Publications: 3 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.872 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.-110+67390A>G		intron_variant	Intron 1 of 3	4		ENSP00000425858.1
GPR141	ENST00000461610.5	n.232+65710A>G		intron_variant	Intron 2 of 3	1

Frequencies

GnomAD3 genomes AF: 0.847 AC: 128434 AN: 151610 Hom.: 54448 Cov.: 28

Gnomad AFR AF: 0.831

Gnomad AMI AF: 0.878

Gnomad AMR AF: 0.884

Gnomad ASJ AF: 0.854

Gnomad EAS AF: 0.813

Gnomad SAS AF: 0.824

Gnomad FIN AF: 0.879

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.847

Gnomad OTH AF: 0.844

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

GnomAD4 genome AF: 0.847 AC: 128528 AN: 151726 Hom.: 54486 Cov.: 28 AF XY: 0.849 AC XY: 62919 AN XY: 74134

African (AFR) AF: 0.831 AC: 34382 AN: 41378

American (AMR) AF: 0.884 AC: 13471 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.854 AC: 2965 AN: 3470

East Asian (EAS) AF: 0.814 AC: 4189 AN: 5148

South Asian (SAS) AF: 0.824 AC: 3961 AN: 4808

European-Finnish (FIN) AF: 0.879 AC: 9193 AN: 10464

Middle Eastern (MID) AF: 0.878 AC: 258 AN: 294

European-Non Finnish (NFE) AF: 0.847 AC: 57535 AN: 67914

Other (OTH) AF: 0.844 AC: 1775 AN: 2104

Alfa AF: 0.842 Hom.: 29578

Bravo AF: 0.847

Asia WGS AF: 0.828 AC: 2879 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.30
DANN	Benign	0.64
PhyloP100		-0.69
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: rs2709114; hg19: chr7-37790895;