rs1982389

Positions:

• chr7-37687349-A-G

Variant summary

Our verdict is Benign. Variant got -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

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=-0.91).
• 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 male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 114 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GPR141	NM_001381946.1	c.-15+1766A>G		intron_variant		ENST00000334425.2	NP_001368875.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GPR141	ENST00000334425.2	c.-15+1766A>G		intron_variant			NM_001381946.1	ENSP00000334540	P1

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

Gnomad4 AFR AF: 0.00993

Gnomad4 AMR AF: 0.0307

Gnomad4 ASJ AF: 0.0568

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0131

Gnomad4 FIN AF: 0.0202

Gnomad4 NFE AF: 0.0505

Gnomad4 OTH AF: 0.0407

Alfa AF: 0.0491 Hom.: 237

Bravo AF: 0.0329

Asia WGS AF: 0.00924 AC: 32 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.050
DANN	Benign	0.48

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

Publications

LitVar

Other links and lift over

dbSNP: rs1982389; hg19: chr7-37726951;