Genetic Variant NM_005290.4:c.-16C>A (chr3-98532018-C-A) – 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.-16C>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 1,582,760 control chromosomes in the GnomAD database, including 11,722 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 0.10 ( 934 hom., cov: 32)

Exomes 𝑓: 0.12 ( 10788 hom. )

Consequence

GPR15
NM_005290.4 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.110

Publications

16 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 (BayesDel_noAF=-0.83).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.133 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GPR15	NM_005290.4 link	c.-16C>A		5_prime_UTR_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.-16C>A		5_prime_UTR_variant	Exon 1 of 1	6	NM_005290.4	ENSP00000284311.3		P49685
ENSG00000285635	ENST00000512905.6 link	n.*71-10576G>T		intron_variant	Intron 3 of 3	5		ENSP00000425880.1		H0YA22

Frequencies

GnomAD3 genomes

AF:

0.104

AC:

15760

AN:

152092

Hom.:

929

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0594

Gnomad AMI

AF:

0.190

Gnomad AMR

AF:

0.120

Gnomad ASJ

AF:

0.0684

Gnomad EAS

AF:

0.139

Gnomad SAS

AF:

0.142

Gnomad FIN

AF:

0.122

Gnomad MID

AF:

0.0981

Gnomad NFE

AF:

0.119

Gnomad OTH

AF:

0.104

GnomAD2 exomes

AF:

0.120

AC:

27829

AN:

232824

AF XY:

0.120

show subpopulations

Gnomad AFR exome

AF:

0.0610

Gnomad AMR exome

AF:

0.136

Gnomad ASJ exome

AF:

0.0716

Gnomad EAS exome

AF:

0.119

Gnomad FIN exome

AF:

0.120

Gnomad NFE exome

AF:

0.122

Gnomad OTH exome

AF:

0.121

GnomAD4 exome

AF:

0.121

AC:

172985

AN:

1430550

Hom.:

10788

Cov.:

AF XY:

0.121

AC XY:

85316

AN XY:

707778

show subpopulations

African (AFR)

AF:

0.0590

AC:

1912

AN:

32386

American (AMR)

AF:

0.132

AC:

5331

AN:

40396

Ashkenazi Jewish (ASJ)

AF:

0.0688

AC:

1698

AN:

24680

East Asian (EAS)

AF:

0.152

AC:

5974

AN:

39234

South Asian (SAS)

AF:

0.132

AC:

10753

AN:

81658

European-Finnish (FIN)

AF:

0.123

AC:

6468

AN:

52682

Middle Eastern (MID)

AF:

0.0882

AC:

495

AN:

5612

European-Non Finnish (NFE)

AF:

0.122

AC:

133413

AN:

1095018

Other (OTH)

AF:

0.118

AC:

6941

AN:

58884

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.471

Heterozygous variant carriers

6905

13810

20716

27621

34526

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4928

9856

14784

19712

24640

<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:

0.104

AC:

15793

AN:

152210

Hom.:

934

Cov.:

AF XY:

0.106

AC XY:

7858

AN XY:

74422

show subpopulations

African (AFR)

AF:

0.0596

AC:

2474

AN:

41536

American (AMR)

AF:

0.120

AC:

1838

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.0684

AC:

237

AN:

3464

East Asian (EAS)

AF:

0.139

AC:

722

AN:

5180

South Asian (SAS)

AF:

0.142

AC:

685

AN:

4816

European-Finnish (FIN)

AF:

0.122

AC:

1296

AN:

10598

Middle Eastern (MID)

AF:

0.102

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.119

AC:

8111

AN:

67992

Other (OTH)

AF:

0.107

AC:

227

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

712

1425

2137

2850

3562

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

186

372

558

744

930

<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:

0.113

Hom.:

1968

Bravo

AF:

0.0993

Asia WGS

AF:

0.185

AC:

642

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

4.5

(source)

DANN

Benign

0.59

PhyloP100

0.11

PromoterAI

0.018

Neutral

(source)

Mutation Taster

=299/1

polymorphism (auto)

(source)

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

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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