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

Variant summary

Our verdict is Benign. The variant received -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

Publications

2 publications found

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 was made for transcript

Our verdict: Benign. The variant received -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 VariationId 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152529.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
GPR155	NM_152529.7	MANE Select	c.2136A>G	p.Gly712Gly	synonymous	Exon 14 of 16	NP_689742.4
GPR155	NM_001033045.4		c.2136A>G	p.Gly712Gly	synonymous	Exon 15 of 17	NP_001028217.1	Q7Z3F1
GPR155	NM_001267050.2		c.2136A>G	p.Gly712Gly	synonymous	Exon 15 of 17	NP_001253979.1	Q7Z3F1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
GPR155	ENST00000392552.7	TSL:1 MANE Select	c.2136A>G	p.Gly712Gly	synonymous	Exon 14 of 16	ENSP00000376335.2	Q7Z3F1
GPR155	ENST00000295500.8	TSL:1	c.2136A>G	p.Gly712Gly	synonymous	Exon 15 of 17	ENSP00000295500.4	Q7Z3F1
GPR155	ENST00000392551.6	TSL:1	c.2136A>G	p.Gly712Gly	synonymous	Exon 15 of 17	ENSP00000376334.2	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

GnomAD2 exomes

AF:

0.00666

AC:

1658

AN:

249120

AF XY:

0.00569

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 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

African (AFR)

AF:

0.0640

AC:

1835

AN:

28672

American (AMR)

AF:

0.00389

AC:

170

AN:

43742

Ashkenazi Jewish (ASJ)

AF:

0.00732

AC:

178

AN:

24322

East Asian (EAS)

AF:

0.00387

AC:

149

AN:

38500

South Asian (SAS)

AF:

0.00611

AC:

497

AN:

81366

European-Finnish (FIN)

AF:

0.000170

AC:

AN:

53042

Middle Eastern (MID)

AF:

0.00809

AC:

AN:

5314

European-Non Finnish (NFE)

AF:

0.000330

AC:

298

AN:

902596

Other (OTH)

AF:

0.00587

AC:

306

AN:

52172

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.441

Heterozygous variant carriers

149

298

447

596

745

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

120

180

240

300

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0214

AC:

3262

AN:

152266

Hom.:

104

Cov.:

AF XY:

0.0210

AC XY:

1565

AN XY:

74454

show subpopulations

African (AFR)

AF:

0.0711

AC:

2953

AN:

41538

American (AMR)

AF:

0.00929

AC:

142

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.0112

AC:

AN:

3472

East Asian (EAS)

AF:

0.00444

AC:

AN:

5186

South Asian (SAS)

AF:

0.00890

AC:

AN:

4832

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10602

Middle Eastern (MID)

AF:

0.0102

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.000544

AC:

AN:

68028

Other (OTH)

AF:

0.0104

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

159

318

478

637

796

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

108

144

180

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0102

Hom.:

Bravo

AF:

0.0243

Asia WGS

AF:

0.0200

AC:

AN:

3478

EpiCase

AF:

0.00125

EpiControl

AF:

0.00124

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (2)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.46

CADD

Benign

7.5

(source)

DANN

Benign

0.71

PhyloP100

-0.85

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over