10-25465852-C-T

Variant names:

• chr10-25465852-C-T
• rs1620326
• NM_020752.3:c.1336-799C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.776 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GPR158	NM_020752.3	MANE Select	c.1336-799C>T		intron	N/A	NP_065803.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GPR158	ENST00000376351.4	TSL:1 MANE Select	c.1336-799C>T		intron	N/A	ENSP00000365529.3
	GPR158	ENST00000650135.1		c.1099-799C>T		intron	N/A	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

African (AFR) AF: 0.292 AC: 12101 AN: 41462

American (AMR) AF: 0.496 AC: 7573 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.575 AC: 1993 AN: 3468

East Asian (EAS) AF: 0.797 AC: 4088 AN: 5132

South Asian (SAS) AF: 0.543 AC: 2619 AN: 4824

European-Finnish (FIN) AF: 0.596 AC: 6288 AN: 10548

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.527 AC: 35795 AN: 67964

Other (OTH) AF: 0.505 AC: 1068 AN: 2114

Alfa AF: 0.478 Hom.: 3159

Bravo AF: 0.461

Asia WGS AF: 0.587 AC: 2038 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	9.3
DANN	Benign	0.82
PhyloP100		-0.18
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: rs1620326; hg19: chr10-25754781;