rs17558301

Variant names:

• chr10-25591530-C-G
• rs17558301
• NM_020752.3:c.1892+2385C>G

Variant summary

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

The NM_020752.3(GPR158):​c.1892+2385C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.043 in 152,112 control chromosomes in the GnomAD database, including 203 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 0.043 (203 hom., cov: 32)
• Consequence: GPR158 NM_020752.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.78
• Publications: 1 publications found

Genes affected

GPR158 (HGNC:23689): (G protein-coupled receptor 158) Predicted to enable G protein-coupled receptor activity. Predicted to act upstream of or within G protein-coupled receptor signaling pathway and protein localization to plasma membrane. Predicted to be located in membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0559 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020752.3. 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
	GPR158	NM_020752.3	MANE Select	c.1892+2385C>G		intron	N/A	NP_065803.2	Q5T848

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GPR158	ENST00000376351.4	TSL:1 MANE Select	c.1892+2385C>G		intron	N/A	ENSP00000365529.3	Q5T848
	GPR158	ENST00000650135.1		c.1655+2385C>G		intron	N/A	ENSP00000498176.1	A0A3B3IUC3

Frequencies

GnomAD3 genomes AF: 0.0431 AC: 6547 AN: 151994 Hom.: 202 Cov.: 32

Gnomad AFR AF: 0.0101

Gnomad AMI AF: 0.0899

Gnomad AMR AF: 0.0431

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0609

Gnomad FIN AF: 0.0670

Gnomad MID AF: 0.0701

Gnomad NFE AF: 0.0574

Gnomad OTH AF: 0.0531

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

GnomAD4 genome AF: 0.0430 AC: 6548 AN: 152112 Hom.: 203 Cov.: 32 AF XY: 0.0433 AC XY: 3216 AN XY: 74358

African (AFR) AF: 0.0101 AC: 418 AN: 41530

American (AMR) AF: 0.0430 AC: 657 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 349 AN: 3472

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5186

South Asian (SAS) AF: 0.0614 AC: 296 AN: 4822

European-Finnish (FIN) AF: 0.0670 AC: 709 AN: 10578

Middle Eastern (MID) AF: 0.0719 AC: 21 AN: 292

European-Non Finnish (NFE) AF: 0.0574 AC: 3902 AN: 67938

Other (OTH) AF: 0.0526 AC: 111 AN: 2112

Alfa AF: 0.0492 Hom.: 27

Bravo AF: 0.0395

Asia WGS AF: 0.0240 AC: 85 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.6
DANN	Benign	0.75
PhyloP100		1.8
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: rs17558301; hg19: chr10-25880459;