ENST00000476620.1:c.-109-37453C>T

Variant names:

• chr7-37819821-C-T
• rs10241576
• ENST00000476620.1:c.-109-37453C>T

Variant summary

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

The ENST00000476620.1(ENSG00000290149):​c.-109-37453C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 152,062 control chromosomes in the GnomAD database, including 6,742 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 0.28 (6742 hom., cov: 32)
• Consequence: ENSG00000290149 ENST00000476620.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• 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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.357 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.-109-37453C>T		intron_variant	Intron 1 of 3	4		ENSP00000425858.1
GPR141	ENST00000461610.5	n.233-9434C>T		intron_variant	Intron 2 of 3	1

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42438 AN: 151944 Hom.: 6748 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.382

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.279 AC: 42423 AN: 152062 Hom.: 6742 Cov.: 32 AF XY: 0.279 AC XY: 20740 AN XY: 74322

African (AFR) AF: 0.125 AC: 5190 AN: 41502

American (AMR) AF: 0.276 AC: 4218 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.356 AC: 1234 AN: 3466

East Asian (EAS) AF: 0.208 AC: 1074 AN: 5170

South Asian (SAS) AF: 0.333 AC: 1606 AN: 4822

European-Finnish (FIN) AF: 0.318 AC: 3350 AN: 10550

Middle Eastern (MID) AF: 0.373 AC: 109 AN: 292

European-Non Finnish (NFE) AF: 0.361 AC: 24547 AN: 67960

Other (OTH) AF: 0.299 AC: 632 AN: 2112

Alfa AF: 0.331 Hom.: 27142

Bravo AF: 0.267

Asia WGS AF: 0.233 AC: 807 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.21
DANN	Benign	0.65
PhyloP100		-1.4
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: rs10241576; hg19: chr7-37859423;