rs6951258

Variant names:

• chr7-37717954-T-C
• rs6951258
• NM_001381946.1:c.-14-22426T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001381946.1(GPR141):​c.-14-22426T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.061 in 152,232 control chromosomes in the GnomAD database, including 972 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 0.061 (972 hom., cov: 31)
• Consequence: GPR141 NM_001381946.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.770
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.207 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GPR141	NM_001381946.1	MANE Select	c.-14-22426T>C		intron	N/A	NP_001368875.1	Q7Z602
	GPR141	NM_001329993.2		c.-137-11962T>C		intron	N/A	NP_001316922.1	Q7Z602
	GPR141	NM_001329994.2		c.-14-22426T>C		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.-14-22426T>C		intron	N/A	ENSP00000334540.1	Q7Z602
	ENSG00000290149	ENST00000476620.1	TSL:4	c.-110+34051T>C		intron	N/A	ENSP00000425858.1	D6RIH7
	GPR141	ENST00000461610.5	TSL:1	n.232+32371T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0608 AC: 9250 AN: 152114 Hom.: 969 Cov.: 31

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0243

Gnomad ASJ AF: 0.00115

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00104

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00110

Gnomad OTH AF: 0.0435

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

GnomAD4 genome AF: 0.0610 AC: 9280 AN: 152232 Hom.: 972 Cov.: 31 AF XY: 0.0584 AC XY: 4346 AN XY: 74440

African (AFR) AF: 0.210 AC: 8728 AN: 41490

American (AMR) AF: 0.0242 AC: 370 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.00115 AC: 4 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5190

South Asian (SAS) AF: 0.000830 AC: 4 AN: 4822

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10614

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.00110 AC: 75 AN: 68034

Other (OTH) AF: 0.0430 AC: 91 AN: 2114

Alfa AF: 0.0513 Hom.: 742

Bravo AF: 0.0695

Asia WGS AF: 0.0140 AC: 48 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	0.41
DANN	Benign	0.46
PhyloP100		-0.77
Mutation Taster		=100/0	polymorphism (auto)

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: rs6951258; hg19: chr7-37757556;