rs10241576

Positions:

• chr7-37819821-C-T

Variant summary

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

The ENST00000461610.5(GPR141):​n.233-9434C>T 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 0.279 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: GPR141 ENST00000461610.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36

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=-0.98).
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GPR141	ENST00000461610.5	n.233-9434C>T		intron_variant, non_coding_transcript_variant		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;