rs17558301

Positions:

• chr10-25591530-C-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GPR158	NM_020752.3	c.1892+2385C>G		intron_variant		ENST00000376351.4
GPR158	XM_017016452.3	c.332+2385C>G		intron_variant
GPR158	XR_930512.4	n.2312+2385C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GPR158	ENST00000376351.4	c.1892+2385C>G		intron_variant		1	NM_020752.3	P2
GPR158	ENST00000650135.1	c.1655+2385C>G		intron_variant				A2

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

Gnomad4 AFR AF: 0.0101

Gnomad4 AMR AF: 0.0430

Gnomad4 ASJ AF: 0.101

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0614

Gnomad4 FIN AF: 0.0670

Gnomad4 NFE AF: 0.0574

Gnomad4 OTH AF: 0.0526

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.6
DANN	Benign	0.75

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: rs17558301; hg19: chr10-25880459;