rs117372847

Variant names:

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_002564.4(P2RY2):c.50A>G(p.Asp17Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00592 in 1,613,886 control chromosomes in the GnomAD database, including 63 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. D17D) has been classified as Benign.

Frequency

Genomes: 𝑓 0.0055 ( 10 hom., cov: 33)

Exomes 𝑓: 0.0060 ( 53 hom. )

Consequence

P2RY2
NM_002564.4 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.439

Publications

7 publications found

Variant links:

Genes affected

P2RY2 (HGNC:8541): (purinergic receptor P2Y2) The product of this gene belongs to the family of P2 receptors, which is activated by extracellular nucleotides and subdivided into P2X ligand-gated ion channels and P2Y G-protein coupled receptors. This family has several receptor subtypes with different pharmacological selectivity, which overlaps in some cases, for various adenosine and uridine nucleotides. This receptor, found on many cell types, is activated by ATP and UTP and is reported to be overexpressed on some cancer cell types. It is involved in many cellular functions, such as proliferation, apoptosis and inflammation. Three transcript variants encoding the same protein have been identified for this gene. [provided by RefSeq, Mar 2013]

P2RY2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0034140348).

BP6

Variant 11-73234209-A-G is Benign according to our data. Variant chr11-73234209-A-G is described in ClinVar as Likely_benign. ClinVar VariationId is 2642132.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 10 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002564.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
P2RY2	NM_002564.4	MANE Select	c.50A>G	p.Asp17Gly	missense	Exon 3 of 3	NP_002555.4
P2RY2	NM_176071.3		c.50A>G	p.Asp17Gly	missense	Exon 3 of 3	NP_788085.3	P41231
P2RY2	NM_176072.3		c.50A>G	p.Asp17Gly	missense	Exon 3 of 3	NP_788086.3	P41231

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
P2RY2	ENST00000393597.7	TSL:1 MANE Select	c.50A>G	p.Asp17Gly	missense	Exon 3 of 3	ENSP00000377222.2	P41231
P2RY2	ENST00000311131.6	TSL:1	c.50A>G	p.Asp17Gly	missense	Exon 3 of 3	ENSP00000310305.2	P41231
P2RY2	ENST00000393596.2	TSL:1	c.50A>G	p.Asp17Gly	missense	Exon 3 of 3	ENSP00000377221.2	P41231

Frequencies

GnomAD3 genomes

AF:

0.00550

AC:

836

AN:

152042

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000870

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00347

Gnomad ASJ

AF:

0.0357

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00104

Gnomad FIN

AF:

0.00699

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00791

Gnomad OTH

AF:

0.00287

GnomAD2 exomes

AF:

0.00519

AC:

1304

AN:

251038

AF XY:

0.00507

show subpopulations

Gnomad AFR exome

AF:

0.000923

Gnomad AMR exome

AF:

0.00156

Gnomad ASJ exome

AF:

0.0300

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00680

Gnomad NFE exome

AF:

0.00634

Gnomad OTH exome

AF:

0.00522

GnomAD4 exome

AF:

0.00596

AC:

8719

AN:

1461726

Hom.:

Cov.:

AF XY:

0.00597

AC XY:

4344

AN XY:

727170

show subpopulations

African (AFR)

AF:

0.000687

AC:

AN:

33478

American (AMR)

AF:

0.00177

AC:

AN:

44710

Ashkenazi Jewish (ASJ)

AF:

0.0298

AC:

779

AN:

26118

East Asian (EAS)

AF:

0.00

AC:

AN:

39700

South Asian (SAS)

AF:

0.00147

AC:

127

AN:

86246

European-Finnish (FIN)

AF:

0.00768

AC:

410

AN:

53400

Middle Eastern (MID)

AF:

0.00156

AC:

AN:

5766

European-Non Finnish (NFE)

AF:

0.00620

AC:

6894

AN:

1111918

Other (OTH)

AF:

0.00659

AC:

398

AN:

60390

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.480

Heterozygous variant carriers

469

939

1408

1878

2347

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

252

504

756

1008

1260

<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:

0.00549

AC:

836

AN:

152160

Hom.:

Cov.:

AF XY:

0.00531

AC XY:

395

AN XY:

74400

show subpopulations

African (AFR)

AF:

0.000867

AC:

AN:

41512

American (AMR)

AF:

0.00347

AC:

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.0357

AC:

124

AN:

3470

East Asian (EAS)

AF:

0.00

AC:

AN:

5164

South Asian (SAS)

AF:

0.00104

AC:

AN:

4826

European-Finnish (FIN)

AF:

0.00699

AC:

AN:

10592

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00791

AC:

538

AN:

67986

Other (OTH)

AF:

0.00284

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

137

182

228

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

<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:

0.00716

Hom.:

Bravo

AF:

0.00468

TwinsUK

AF:

0.00431

AC:

ALSPAC

AF:

0.00234

AC:

ESP6500AA

AF:

0.00182

AC:

ESP6500EA

AF:

0.00804

AC:

ExAC

AF:

0.00526

AC:

638

ClinVar

ClinVar submissions

Significance:Likely benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.066

BayesDel_addAF

Benign

-0.58

BayesDel_noAF

Benign

-0.59

CADD

Benign

(source)

DANN

Benign

0.96

DEOGEN2

Benign

0.049

Eigen

Benign

-0.67

Eigen_PC

Benign

-0.60

FATHMM_MKL

Benign

0.14

LIST_S2

Benign

0.61

M_CAP

Benign

0.0045

MetaRNN

Benign

0.0034

MetaSVM

Benign

-1.0

MutationAssessor

Benign

1.5

PhyloP100

0.44

PrimateAI

Benign

0.31

PROVEAN

Benign

-0.28

REVEL

Benign

0.035

Sift

Benign

0.33

Sift4G

Benign

0.082

Polyphen

0.0

Vest4

0.11

MVP

0.50

MPC

0.46

ClinPred

0.0056

GERP RS

1.0

Varity_R

0.071

gMVP

0.50

Mutation Taster

=96/4

polymorphism

(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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over