NM_001381946.1:c.-15+1766A>G

Variant names:

• chr7-37687349-A-G
• rs1982389
• NM_001381946.1:c.-15+1766A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_001381946.1(GPR141):​c.-15+1766A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0323 in 152,246 control chromosomes in the GnomAD database, including 114 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 0.032 (114 hom., cov: 32)
• Consequence: GPR141 NM_001381946.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66
• Publications: 1 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=-0.91).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0323 (4917/152246) while in subpopulation NFE AF = 0.0505 (3437/68026). AF 95% confidence interval is 0.0491. There are 114 homozygotes in GnomAd4. There are 2258 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 114 AR gene

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GPR141	NM_001381946.1	MANE Select	c.-15+1766A>G		intron	N/A	NP_001368875.1	Q7Z602
	GPR141	NM_001329993.2		c.-138+1766A>G		intron	N/A	NP_001316922.1	Q7Z602
	GPR141	NM_001329994.2		c.-15+1766A>G		intron	N/A	NP_001316923.1	Q7Z602

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GPR141	ENST00000334425.2	TSL:6 MANE Select	c.-15+1766A>G		intron	N/A	ENSP00000334540.1	Q7Z602
	ENSG00000290149	ENST00000476620.1	TSL:4	c.-110+3446A>G		intron	N/A	ENSP00000425858.1	D6RIH7
	GPR141	ENST00000461610.5	TSL:1	n.232+1766A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0323 AC: 4919 AN: 152128 Hom.: 114 Cov.: 32

Gnomad AFR AF: 0.00996

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.0308

Gnomad ASJ AF: 0.0568

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0133

Gnomad FIN AF: 0.0202

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0505

Gnomad OTH AF: 0.0411

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

GnomAD4 genome AF: 0.0323 AC: 4917 AN: 152246 Hom.: 114 Cov.: 32 AF XY: 0.0303 AC XY: 2258 AN XY: 74444

African (AFR) AF: 0.00993 AC: 412 AN: 41506

American (AMR) AF: 0.0307 AC: 470 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0568 AC: 197 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5190

South Asian (SAS) AF: 0.0131 AC: 63 AN: 4820

European-Finnish (FIN) AF: 0.0202 AC: 214 AN: 10620

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0505 AC: 3437 AN: 68026

Other (OTH) AF: 0.0407 AC: 86 AN: 2112

Alfa AF: 0.0449 Hom.: 540

Bravo AF: 0.0329

Asia WGS AF: 0.00924 AC: 32 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.050
DANN	Benign	0.48
PhyloP100		-1.7
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1982389; hg19: chr7-37726951;