rs10241576

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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=-0.98).
• 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

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.276

Gnomad4 ASJ AF: 0.356

Gnomad4 EAS AF: 0.208

Gnomad4 SAS AF: 0.333

Gnomad4 FIN AF: 0.318

Gnomad4 NFE AF: 0.361

Gnomad4 OTH AF: 0.299

Alfa AF: 0.347 Hom.: 18703

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10241576; hg19: chr7-37859423;