dbSNP rs2230344: GPR15:p.Pro37Ser (chr3-98532142-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_005290.4(GPR15):c.109C>T(p.Pro37Ser) variant causes a missense change. The variant allele was found at a frequency of 0.16 in 1,613,950 control chromosomes in the GnomAD database, including 24,252 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 0.14 ( 2066 hom., cov: 32)

Exomes 𝑓: 0.16 ( 22186 hom. )

Consequence

GPR15
NM_005290.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.02

Publications

24 publications found

Variant links:

Genes affected

GPR15 (HGNC:4469): (G protein-coupled receptor 15) This gene encodes a G protein-coupled receptor that acts as a chemokine receptor for human immunodeficiency virus type 1 and 2. The encoded protein localizes to the cell membrane. [provided by RefSeq, Nov 2012]

GPR15 links:

ENSG00000285635 (HGNC:):

ENSG00000285635 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0018767416).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.358 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GPR15	NM_005290.4 link	c.109C>T	p.Pro37Ser	missense_variant	Exon 1 of 1	ENST00000284311.5	NP_005281.1	P49685B6V9G9B2R8H6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GPR15	ENST00000284311.5 link	c.109C>T	p.Pro37Ser	missense_variant	Exon 1 of 1	6	NM_005290.4	ENSP00000284311.3		P49685
ENSG00000285635	ENST00000512905.6 link	n.*71-10700G>A		intron_variant	Intron 3 of 3	5		ENSP00000425880.1		H0YA22

Frequencies

GnomAD3 genomes

AF:

0.142

AC:

21567

AN:

152054

Hom.:

2068

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0496

Gnomad AMI

AF:

0.0407

Gnomad AMR

AF:

0.264

Gnomad ASJ

AF:

0.145

Gnomad EAS

AF:

0.372

Gnomad SAS

AF:

0.222

Gnomad FIN

AF:

0.136

Gnomad MID

AF:

0.250

Gnomad NFE

AF:

0.149

Gnomad OTH

AF:

0.143

GnomAD2 exomes

AF:

0.201

AC:

50481

AN:

251398

AF XY:

0.198

show subpopulations

Gnomad AFR exome

AF:

0.0466

Gnomad AMR exome

AF:

0.376

Gnomad ASJ exome

AF:

0.151

Gnomad EAS exome

AF:

0.390

Gnomad FIN exome

AF:

0.134

Gnomad NFE exome

AF:

0.150

Gnomad OTH exome

AF:

0.180

GnomAD4 exome

AF:

0.162

AC:

237408

AN:

1461778

Hom.:

22186

Cov.:

AF XY:

0.164

AC XY:

119407

AN XY:

727218

show subpopulations

African (AFR)

AF:

0.0440

AC:

1474

AN:

33480

American (AMR)

AF:

0.365

AC:

16322

AN:

44714

Ashkenazi Jewish (ASJ)

AF:

0.149

AC:

3906

AN:

26136

East Asian (EAS)

AF:

0.361

AC:

14337

AN:

39698

South Asian (SAS)

AF:

0.230

AC:

19863

AN:

86256

European-Finnish (FIN)

AF:

0.131

AC:

6978

AN:

53420

Middle Eastern (MID)

AF:

0.197

AC:

1139

AN:

5768

European-Non Finnish (NFE)

AF:

0.147

AC:

163208

AN:

1111916

Other (OTH)

AF:

0.169

AC:

10181

AN:

60390

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.478

Heterozygous variant carriers

11247

22493

33740

44986

56233

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

6082

12164

18246

24328

30410

<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:

0.142

AC:

21563

AN:

152172

Hom.:

2066

Cov.:

AF XY:

0.147

AC XY:

10959

AN XY:

74380

show subpopulations

African (AFR)

AF:

0.0495

AC:

2058

AN:

41544

American (AMR)

AF:

0.265

AC:

4044

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.145

AC:

502

AN:

3472

East Asian (EAS)

AF:

0.371

AC:

1922

AN:

5174

South Asian (SAS)

AF:

0.223

AC:

1075

AN:

4812

European-Finnish (FIN)

AF:

0.136

AC:

1437

AN:

10582

Middle Eastern (MID)

AF:

0.235

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.149

AC:

10122

AN:

67986

Other (OTH)

AF:

0.141

AC:

297

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

905

1811

2716

3622

4527

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

246

492

738

984

1230

<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:

0.153

Hom.:

6836

Bravo

AF:

0.148

TwinsUK

AF:

0.138

AC:

513

ALSPAC

AF:

0.149

AC:

574

ESP6500AA

AF:

0.0508

AC:

224

ESP6500EA

AF:

0.152

AC:

1304

ExAC

AF:

0.191

AC:

23185

Asia WGS

AF:

0.213

AC:

737

AN:

3478

EpiCase

AF:

0.158

EpiControl

AF:

0.156

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.41

BayesDel_addAF

Benign

-0.59

BayesDel_noAF

Benign

-0.48

CADD

Benign

(source)

DANN

Uncertain

0.98

DEOGEN2

Benign

0.13

Eigen

Benign

-0.14

Eigen_PC

Benign

-0.055

FATHMM_MKL

Uncertain

0.91

LIST_S2

Benign

0.72

MetaRNN

Benign

0.0019

MetaSVM

Benign

-0.96

MutationAssessor

Benign

1.3

PhyloP100

5.0

PrimateAI

Benign

0.46

PROVEAN

Pathogenic

-7.6

REVEL

Benign

0.13

Sift

Benign

0.056

Sift4G

Benign

0.20

Polyphen

0.21

Vest4

0.084

MPC

0.082

ClinPred

0.048

GERP RS

3.9

PromoterAI

0.025

Neutral

(source)

Varity_R

0.32

gMVP

0.51

Mutation Taster

=79/21

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over