10-25465852-C-T

Position:

• chr10-25465852-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020752.3(GPR158):​c.1336-799C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.475 in 151,982 control chromosomes in the GnomAD database, including 18,287 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 0.48 (18287 hom., cov: 32)
• Consequence: GPR158 NM_020752.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.181

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]

GPR158 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.776 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GPR158	NM_020752.3	c.1336-799C>T		intron_variant		ENST00000376351.4	NP_065803.2
GPR158	XR_930512.4	n.1756-799C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GPR158	ENST00000376351.4	c.1336-799C>T		intron_variant		1	NM_020752.3	ENSP00000365529.3
GPR158	ENST00000650135.1	c.1099-799C>T		intron_variant				ENSP00000498176.1

Frequencies

GnomAD3 genomes AF: 0.476 AC: 72220 AN: 151864 Hom.: 18288 Cov.: 32

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.575

Gnomad EAS AF: 0.796

Gnomad SAS AF: 0.543

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.506

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

GnomAD4 genome AF: 0.475 AC: 72245 AN: 151982 Hom.: 18287 Cov.: 32 AF XY: 0.480 AC XY: 35688 AN XY: 74274

Gnomad4 AFR AF: 0.292

Gnomad4 AMR AF: 0.496

Gnomad4 ASJ AF: 0.575

Gnomad4 EAS AF: 0.797

Gnomad4 SAS AF: 0.543

Gnomad4 FIN AF: 0.596

Gnomad4 NFE AF: 0.527

Gnomad4 OTH AF: 0.505

Alfa AF: 0.483 Hom.: 3123

Bravo AF: 0.461

Asia WGS AF: 0.587 AC: 2038 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	9.3
DANN	Benign	0.82

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: rs1620326; hg19: chr10-25754781;