rs7780507

chr7-37743498-C-Achr7-37743498-C-T

Variant summary

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

The NM_001381946.1(GPR141):c.*2187C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.765 in 151,566 control chromosomes in the GnomAD database, including 44,613 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 0.77 (44613 hom., cov: 31)
• Consequence: GPR141 NM_001381946.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03

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=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.812 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GPR141	NM_001381946.1	c.*2187C>A		3_prime_UTR_variant	3/3	ENST00000334425.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GPR141	ENST00000334425.2	c.*2187C>A		3_prime_UTR_variant	3/3		NM_001381946.1	P1
GPR141	ENST00000461610.5	n.232+57915C>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.765 AC: 115911 AN: 151448 Hom.: 44590 Cov.: 31

Gnomad AFR AF: 0.683

Gnomad AMI AF: 0.838

Gnomad AMR AF: 0.823

Gnomad ASJ AF: 0.776

Gnomad EAS AF: 0.800

Gnomad SAS AF: 0.792

Gnomad FIN AF: 0.752

Gnomad MID AF: 0.822

Gnomad NFE AF: 0.798

Gnomad OTH AF: 0.768

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

GnomAD4 genome AF: 0.765 AC: 115986 AN: 151566 Hom.: 44613 Cov.: 31 AF XY: 0.764 AC XY: 56595 AN XY: 74042

Gnomad4 AFR AF: 0.683

Gnomad4 AMR AF: 0.824

Gnomad4 ASJ AF: 0.776

Gnomad4 EAS AF: 0.799

Gnomad4 SAS AF: 0.792

Gnomad4 FIN AF: 0.752

Gnomad4 NFE AF: 0.798

Gnomad4 OTH AF: 0.766

Alfa AF: 0.716 Hom.: 2178

Bravo AF: 0.767

Asia WGS AF: 0.766 AC: 2603 AN: 3396

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	1.4
Dann	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7780507; hg19: chr7-37783100;