Variant rs72637739 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_024980.5(GPR157):c.652C>T(p.Arg218Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 1,612,300 control chromosomes in the GnomAD database, including 37,052 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.17 ( 2844 hom., cov: 32)

Exomes 𝑓: 0.21 ( 34208 hom. )

Consequence

GPR157
NM_024980.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.60

Variant links:

Genes affected

GPR157 (HGNC:23687): (G protein-coupled receptor 157) Predicted to enable G protein-coupled receptor activity. Predicted to be involved in positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G protein-coupled signaling pathway and radial glial cell differentiation. Predicted to be located in ciliary membrane. [provided by Alliance of Genome Resources, Apr 2022]

GPR157 links:

GPR157 (HGNC:):

GPR157 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.005061507).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.242 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GPR157	NM_024980.5 linkuse as main transcript	c.652C>T	p.Arg218Cys	missense_variant	3/4	ENST00000377411.5	NP_079256.4	Q5UAW9
GPR157	XM_005263496.6 linkuse as main transcript	c.613C>T	p.Arg205Cys	missense_variant	3/4		XP_005263553.1
GPR157	XM_005263497.6 linkuse as main transcript	c.598-992C>T		intron_variant			XP_005263554.1
GPR157	XR_007063977.1 linkuse as main transcript	n.727C>T		non_coding_transcript_exon_variant	3/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GPR157	ENST00000377411.5 linkuse as main transcript	c.652C>T	p.Arg218Cys	missense_variant	3/4	1	NM_024980.5	ENSP00000366628.4		Q5UAW9
GPR157	ENST00000465853.1 linkuse as main transcript	c.94-992C>T		intron_variant		5		ENSP00000468362.1		K7ERQ3

Frequencies

GnomAD3 genomes

AF:

0.172

AC:

26129

AN:

152024

Hom.:

2844

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0436

Gnomad AMI

AF:

0.327

Gnomad AMR

AF:

0.249

Gnomad ASJ

AF:

0.159

Gnomad EAS

AF:

0.190

Gnomad SAS

AF:

0.145

Gnomad FIN

AF:

0.238

Gnomad MID

AF:

0.187

Gnomad NFE

AF:

0.221

Gnomad OTH

AF:

0.193

GnomAD3 exomes

AF:

0.213

AC:

52536

AN:

246682

Hom.:

6104

AF XY:

0.210

AC XY:

27989

AN XY:

133252

show subpopulations

Gnomad AFR exome

AF:

0.0400

Gnomad AMR exome

AF:

0.314

Gnomad ASJ exome

AF:

0.165

Gnomad EAS exome

AF:

0.201

Gnomad SAS exome

AF:

0.173

Gnomad FIN exome

AF:

0.247

Gnomad NFE exome

AF:

0.217

Gnomad OTH exome

AF:

0.219

GnomAD4 exome

AF:

0.213

AC:

310626

AN:

1460158

Hom.:

34208

Cov.:

AF XY:

0.212

AC XY:

153765

AN XY:

726198

show subpopulations

Gnomad4 AFR exome

AF:

0.0351

Gnomad4 AMR exome

AF:

0.306

Gnomad4 ASJ exome

AF:

0.170

Gnomad4 EAS exome

AF:

0.202

Gnomad4 SAS exome

AF:

0.169

Gnomad4 FIN exome

AF:

0.243

Gnomad4 NFE exome

AF:

0.218

Gnomad4 OTH exome

AF:

0.200

GnomAD4 genome

AF:

0.172

AC:

26120

AN:

152142

Hom.:

2844

Cov.:

AF XY:

0.173

AC XY:

12875

AN XY:

74356

show subpopulations

Gnomad4 AFR

AF:

0.0435

Gnomad4 AMR

AF:

0.249

Gnomad4 ASJ

AF:

0.159

Gnomad4 EAS

AF:

0.189

Gnomad4 SAS

AF:

0.144

Gnomad4 FIN

AF:

0.238

Gnomad4 NFE

AF:

0.221

Gnomad4 OTH

AF:

0.191

Alfa

AF:

0.207

Hom.:

5135

Bravo

AF:

0.168

TwinsUK

AF:

0.214

AC:

795

ALSPAC

AF:

0.210

AC:

808

ESP6500AA

AF:

0.0499

AC:

220

ESP6500EA

AF:

0.220

AC:

1889

ExAC

AF:

0.204

AC:

24776

Asia WGS

AF:

0.159

AC:

553

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.077

BayesDel_addAF

Benign

-0.75

BayesDel_noAF

Benign

-0.70

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.051

Eigen

Benign

-0.93

Eigen_PC

Benign

-0.87

FATHMM_MKL

Benign

0.47

LIST_S2

Benign

0.51

MetaRNN

Benign

0.0051

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.69

PrimateAI

Benign

0.24

PROVEAN

Benign

-1.7

REVEL

Benign

0.050

Sift

Benign

0.037

Sift4G

Uncertain

0.021

Polyphen

0.068

Vest4

0.073

MPC

0.11

ClinPred

0.013

GERP RS

1.8

Varity_R

0.072

gMVP

0.67

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over