10-25426416-C-T

Position:

• chr10-25426416-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.1335+13943C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.7 in 152,036 control chromosomes in the GnomAD database, including 38,241 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 0.70 (38241 hom., cov: 34)
• Consequence: GPR158 NM_020752.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38

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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.792 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GPR158	NM_020752.3	c.1335+13943C>T		intron_variant		ENST00000376351.4
GPR158	XR_930512.4	n.1755+13943C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GPR158	ENST00000376351.4	c.1335+13943C>T		intron_variant		1	NM_020752.3	P2
GPR158	ENST00000650135.1	c.1098+13943C>T		intron_variant				A2

Frequencies

GnomAD3 genomes AF: 0.700 AC: 106332 AN: 151918 Hom.: 38224 Cov.: 34

Gnomad AFR AF: 0.620

Gnomad AMI AF: 0.749

Gnomad AMR AF: 0.603

Gnomad ASJ AF: 0.741

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.732

Gnomad FIN AF: 0.673

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.798

Gnomad OTH AF: 0.708

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

GnomAD4 genome AF: 0.700 AC: 106400 AN: 152036 Hom.: 38241 Cov.: 34 AF XY: 0.688 AC XY: 51120 AN XY: 74324

Gnomad4 AFR AF: 0.620

Gnomad4 AMR AF: 0.603

Gnomad4 ASJ AF: 0.741

Gnomad4 EAS AF: 0.322

Gnomad4 SAS AF: 0.733

Gnomad4 FIN AF: 0.673

Gnomad4 NFE AF: 0.798

Gnomad4 OTH AF: 0.709

Alfa AF: 0.746 Hom.: 5321

Bravo AF: 0.685

Asia WGS AF: 0.528 AC: 1839 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.3
DANN	Benign	0.50

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: rs2149636; hg19: chr10-25715345;