Variant rs3749073 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_005683.4(GPR55):c.584G>T(p.Gly195Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 1,613,682 control chromosomes in the GnomAD database, including 13,471 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.17 ( 3054 hom., cov: 32)

Exomes 𝑓: 0.11 ( 10417 hom. )

Consequence

GPR55
NM_005683.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0200

Variant links:

Genes affected

GPR55 (HGNC:4511): (G protein-coupled receptor 55) This gene belongs to the G-protein-coupled receptor superfamily. The encoded integral membrane protein is a likely cannabinoid receptor. It may be involved in several physiological and pathological processes by activating a variety of signal transduction pathways. [provided by RefSeq, Aug 2013]

GPR55 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0025137067).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.334 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
GPR55	NM_005683.4 linkuse as main transcript	c.584G>T	p.Gly195Val	missense_variant	2/2	ENST00000650999.1	NP_005674.2
GPR55	XM_005246952.5 linkuse as main transcript	c.584G>T	p.Gly195Val	missense_variant	2/2		XP_005247009.1
GPR55	XM_011512175.4 linkuse as main transcript	c.584G>T	p.Gly195Val	missense_variant	2/2		XP_011510477.1
GPR55	XM_011512176.3 linkuse as main transcript	c.584G>T	p.Gly195Val	missense_variant	2/2		XP_011510478.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GPR55	ENST00000650999.1 linkuse as main transcript	c.584G>T	p.Gly195Val	missense_variant	2/2		NM_005683.4	ENSP00000498258	P1

Frequencies

GnomAD3 genomes

AF:

0.165

AC:

25136

AN:

151894

Hom.:

3044

Cov.:

show subpopulations

Gnomad AFR

AF:

0.339

Gnomad AMI

AF:

0.111

Gnomad AMR

AF:

0.0869

Gnomad ASJ

AF:

0.0660

Gnomad EAS

AF:

0.140

Gnomad SAS

AF:

0.194

Gnomad FIN

AF:

0.0939

Gnomad MID

AF:

0.114

Gnomad NFE

AF:

0.0956

Gnomad OTH

AF:

0.147

GnomAD3 exomes

AF:

0.119

AC:

29881

AN:

251412

Hom.:

2591

AF XY:

0.119

AC XY:

16237

AN XY:

135882

show subpopulations

Gnomad AFR exome

AF:

0.349

Gnomad AMR exome

AF:

0.0504

Gnomad ASJ exome

AF:

0.0705

Gnomad EAS exome

AF:

0.127

Gnomad SAS exome

AF:

0.197

Gnomad FIN exome

AF:

0.0953

Gnomad NFE exome

AF:

0.0939

Gnomad OTH exome

AF:

0.104

GnomAD4 exome

AF:

0.108

AC:

158135

AN:

1461670

Hom.:

10417

Cov.:

AF XY:

0.110

AC XY:

80168

AN XY:

727158

show subpopulations

Gnomad4 AFR exome

AF:

0.351

Gnomad4 AMR exome

AF:

0.0551

Gnomad4 ASJ exome

AF:

0.0680

Gnomad4 EAS exome

AF:

0.155

Gnomad4 SAS exome

AF:

0.191

Gnomad4 FIN exome

AF:

0.0986

Gnomad4 NFE exome

AF:

0.0953

Gnomad4 OTH exome

AF:

0.124

GnomAD4 genome

AF:

0.166

AC:

25186

AN:

152012

Hom.:

3054

Cov.:

AF XY:

0.161

AC XY:

11995

AN XY:

74312

show subpopulations

Gnomad4 AFR

AF:

0.339

Gnomad4 AMR

AF:

0.0868

Gnomad4 ASJ

AF:

0.0660

Gnomad4 EAS

AF:

0.140

Gnomad4 SAS

AF:

0.194

Gnomad4 FIN

AF:

0.0939

Gnomad4 NFE

AF:

0.0956

Gnomad4 OTH

AF:

0.149

Alfa

AF:

0.108

Hom.:

2365

Bravo

AF:

0.170

TwinsUK

AF:

0.101

AC:

374

ALSPAC

AF:

0.0939

AC:

362

ESP6500AA

AF:

0.329

AC:

1451

ESP6500EA

AF:

0.0928

AC:

798

ExAC

AF:

0.128

AC:

15504

Asia WGS

AF:

0.233

AC:

809

AN:

3478

EpiCase

AF:

0.0985

EpiControl

AF:

0.0910

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.079

BayesDel_addAF

Benign

-0.70

BayesDel_noAF

Benign

-0.64

CADD

Benign

6.4

DANN

Benign

0.80

DEOGEN2

Benign

0.011

T;T;T;.

Eigen

Benign

-1.0

Eigen_PC

Benign

-0.94

FATHMM_MKL

Benign

0.051

LIST_S2

Benign

0.63

.;T;.;T

MetaRNN

Benign

0.0025

T;T;T;T

MetaSVM

Benign

-0.91

MutationAssessor

Benign

0.69

N;N;N;.

MutationTaster

Benign

0.034

P;P

PrimateAI

Benign

0.27

PROVEAN

Benign

1.0

.;N;N;N

REVEL

Benign

0.031

Sift

Benign

0.097

.;T;T;T

Sift4G

Benign

0.15

T;T;T;T

Polyphen

0.026

B;B;B;.

Vest4

0.059

MPC

0.33

ClinPred

0.0066

GERP RS

-0.72

Varity_R

0.087

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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