Genetic Variant GPR155:p.Gly712Gly (chr2-174442157-T-C) – ACMG Classification: Benign (-19 pts)

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_152529.7(GPR155):c.2136A>G(p.Gly712Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00488 in 1,381,992 control chromosomes in the GnomAD database, including 180 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.021 ( 104 hom., cov: 32)

Exomes 𝑓: 0.0028 ( 76 hom. )

Consequence

GPR155
NM_152529.7 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.847

Variant links:

Genes affected

GPR155 (HGNC:22951): (G protein-coupled receptor 155) Involved in cognition. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

GPR155 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.46).

BP6

Variant 2-174442157-T-C is Benign according to our data. Variant chr2-174442157-T-C is described in ClinVar as [Benign]. Clinvar id is 778014.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.847 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.069 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GPR155	NM_152529.7 link	c.2136A>G	p.Gly712Gly	synonymous_variant	Exon 14 of 16	ENST00000392552.7	NP_689742.4	Q7Z3F1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GPR155	ENST00000392552.7 link	c.2136A>G	p.Gly712Gly	synonymous_variant	Exon 14 of 16	1	NM_152529.7	ENSP00000376335.2		Q7Z3F1

Frequencies

GnomAD3 genomes

AF:

0.0214

AC:

3249

AN:

152148

Hom.:

103

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0711

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00937

Gnomad ASJ

AF:

0.0112

Gnomad EAS

AF:

0.00442

Gnomad SAS

AF:

0.00868

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.000544

Gnomad OTH

AF:

0.00764

GnomAD3 exomes

AF:

0.00666

AC:

1658

AN:

249120

Hom.:

AF XY:

0.00569

AC XY:

769

AN XY:

135114

show subpopulations

Gnomad AFR exome

AF:

0.0719

Gnomad AMR exome

AF:

0.00337

Gnomad ASJ exome

AF:

0.00798

Gnomad EAS exome

AF:

0.00180

Gnomad SAS exome

AF:

0.00644

Gnomad FIN exome

AF:

0.000277

Gnomad NFE exome

AF:

0.000663

Gnomad OTH exome

AF:

0.00428

GnomAD4 exome

AF:

0.00283

AC:

3485

AN:

1229726

Hom.:

Cov.:

AF XY:

0.00276

AC XY:

1716

AN XY:

622282

show subpopulations

Gnomad4 AFR exome

AF:

0.0640

Gnomad4 AMR exome

AF:

0.00389

Gnomad4 ASJ exome

AF:

0.00732

Gnomad4 EAS exome

AF:

0.00387

Gnomad4 SAS exome

AF:

0.00611

Gnomad4 FIN exome

AF:

0.000170

Gnomad4 NFE exome

AF:

0.000330

Gnomad4 OTH exome

AF:

0.00587

GnomAD4 genome

AF:

0.0214

AC:

3262

AN:

152266

Hom.:

104

Cov.:

AF XY:

0.0210

AC XY:

1565

AN XY:

74454

show subpopulations

Gnomad4 AFR

AF:

0.0711

Gnomad4 AMR

AF:

0.00929

Gnomad4 ASJ

AF:

0.0112

Gnomad4 EAS

AF:

0.00444

Gnomad4 SAS

AF:

0.00890

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000544

Gnomad4 OTH

AF:

0.0104

Alfa

AF:

0.00955

Hom.:

Bravo

AF:

0.0243

Asia WGS

AF:

0.0200

AC:

AN:

3478

EpiCase

AF:

0.00125

EpiControl

AF:

0.00124

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Dec 31, 2019

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.46

CADD

Benign

7.5

DANN

Benign

0.71

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over