rs7071606

chr10-25306308-T-A

Variant summary

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

The NM_020752.3(GPR158):c.1008+85151T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 152,162 control chromosomes in the GnomAD database, including 5,267 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 0.20 (5267 hom., cov: 32)
• Consequence: GPR158 NM_020752.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.493

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.466 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GPR158	NM_020752.3	c.1008+85151T>A		intron_variant		ENST00000376351.4
GPR158	XR_930512.4	n.1428+85151T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GPR158	ENST00000376351.4	c.1008+85151T>A		intron_variant		1	NM_020752.3	P2
GPR158	ENST00000650135.1	c.771+85151T>A		intron_variant				A2

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30728 AN: 152044 Hom.: 5250 Cov.: 32

Gnomad AFR AF: 0.471

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.0873

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.0555

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0921

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.202 AC: 30804 AN: 152162 Hom.: 5267 Cov.: 32 AF XY: 0.199 AC XY: 14824 AN XY: 74398

Gnomad4 AFR AF: 0.472

Gnomad4 AMR AF: 0.123

Gnomad4 ASJ AF: 0.0873

Gnomad4 EAS AF: 0.140

Gnomad4 SAS AF: 0.193

Gnomad4 FIN AF: 0.0555

Gnomad4 NFE AF: 0.0921

Gnomad4 OTH AF: 0.185

Alfa AF: 0.152 Hom.: 411

Bravo AF: 0.217

Asia WGS AF: 0.230 AC: 800 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	2.3
Dann	Benign	0.47

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: rs7071606; hg19: chr10-25595237;