rs7071606

Variant names:

• chr10-25306308-T-A
• rs7071606
• NM_020752.3:c.1008+85151T>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 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=-0.88).
• 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 rank	MANE	Protein	UniProt
GPR158	NM_020752.3	c.1008+85151T>A		intron_variant	Intron 2 of 10	ENST00000376351.4	NP_065803.2
GPR158	XR_930512.4	n.1428+85151T>A		intron_variant	Intron 2 of 11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GPR158	ENST00000376351.4	c.1008+85151T>A		intron_variant	Intron 2 of 10	1	NM_020752.3	ENSP00000365529.3
GPR158	ENST00000650135.1	c.771+85151T>A		intron_variant	Intron 3 of 11			ENSP00000498176.1

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

African (AFR) AF: 0.472 AC: 19563 AN: 41468

American (AMR) AF: 0.123 AC: 1887 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0873 AC: 303 AN: 3470

East Asian (EAS) AF: 0.140 AC: 724 AN: 5174

South Asian (SAS) AF: 0.193 AC: 929 AN: 4824

European-Finnish (FIN) AF: 0.0555 AC: 589 AN: 10612

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.0921 AC: 6266 AN: 68002

Other (OTH) AF: 0.185 AC: 390 AN: 2110

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
PhyloP100		-0.49
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: rs7071606; hg19: chr10-25595237;