NM_001381946.1:c.*2187C>A

Variant names:

• chr7-37743498-C-A
• rs7780507
• NM_001381946.1:c.*2187C>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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]

ENSG00000290149 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001381946.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GPR141	NM_001381946.1	MANE Select	c.*2187C>A		3_prime_UTR	Exon 3 of 3	NP_001368875.1
	GPR141	NM_001329993.2		c.*2187C>A		3_prime_UTR	Exon 4 of 4	NP_001316922.1
	GPR141	NM_001329994.2		c.*2187C>A		3_prime_UTR	Exon 4 of 4	NP_001316923.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GPR141	ENST00000334425.2	TSL:6 MANE Select	c.*2187C>A		3_prime_UTR	Exon 3 of 3	ENSP00000334540.1
	ENSG00000290149	ENST00000476620.1	TSL:4	c.-110+59595C>A		intron	N/A	ENSP00000425858.1
	GPR141	ENST00000461610.5	TSL:1	n.232+57915C>A		intron	N/A

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

African (AFR) AF: 0.683 AC: 28239 AN: 41366

American (AMR) AF: 0.824 AC: 12563 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.776 AC: 2691 AN: 3466

East Asian (EAS) AF: 0.799 AC: 4136 AN: 5174

South Asian (SAS) AF: 0.792 AC: 3809 AN: 4812

European-Finnish (FIN) AF: 0.752 AC: 7757 AN: 10314

Middle Eastern (MID) AF: 0.836 AC: 244 AN: 292

European-Non Finnish (NFE) AF: 0.798 AC: 54169 AN: 67874

Other (OTH) AF: 0.766 AC: 1614 AN: 2106

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.4
DANN	Benign	0.19
PhyloP100		1.0
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: rs7780507; hg19: chr7-37783100;