dbSNP rs701265: P2RY1:p.Val262Val (chr3-152836568-A-G) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_002563.5(P2RY1):c.786A>G(p.Val262Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 1,613,912 control chromosomes in the GnomAD database, including 39,010 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 0.31 ( 11352 hom., cov: 32)

Exomes 𝑓: 0.17 ( 27658 hom. )

Consequence

P2RY1
NM_002563.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.964

Publications

47 publications found

Variant links:

Genes affected

P2RY1 (HGNC:8539): (purinergic receptor P2Y1) The product of this gene belongs to the family of 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 functions as a receptor for extracellular ATP and ADP. In platelets binding to ADP leads to mobilization of intracellular calcium ions via activation of phospholipase C, a change in platelet shape, and probably to platelet aggregation. [provided by RefSeq, Jul 2008]

P2RY1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.68).

BP7

Synonymous conserved (PhyloP=-0.964 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
P2RY1	NM_002563.5 link	c.786A>G	p.Val262Val	synonymous_variant	Exon 1 of 1	ENST00000305097.6	NP_002554.1	P47900

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
P2RY1	ENST00000305097.6 link	c.786A>G	p.Val262Val	synonymous_variant	Exon 1 of 1	6	NM_002563.5	ENSP00000304767.3		P47900

Frequencies

GnomAD3 genomes

AF:

0.310

AC:

47054

AN:

151976

Hom.:

11313

Cov.:

show subpopulations

Gnomad AFR

AF:

0.676

Gnomad AMI

AF:

0.266

Gnomad AMR

AF:

0.241

Gnomad ASJ

AF:

0.140

Gnomad EAS

AF:

0.270

Gnomad SAS

AF:

0.193

Gnomad FIN

AF:

0.148

Gnomad MID

AF:

0.209

Gnomad NFE

AF:

0.150

Gnomad OTH

AF:

0.282

GnomAD2 exomes

AF:

0.211

AC:

53037

AN:

251444

AF XY:

0.200

show subpopulations

Gnomad AFR exome

AF:

0.690

Gnomad AMR exome

AF:

0.233

Gnomad ASJ exome

AF:

0.144

Gnomad EAS exome

AF:

0.281

Gnomad FIN exome

AF:

0.149

Gnomad NFE exome

AF:

0.149

Gnomad OTH exome

AF:

0.192

GnomAD4 exome

AF:

0.173

AC:

252456

AN:

1461818

Hom.:

27658

Cov.:

AF XY:

0.172

AC XY:

125055

AN XY:

727218

show subpopulations

African (AFR)

AF:

0.694

AC:

23221

AN:

33476

American (AMR)

AF:

0.236

AC:

10575

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.139

AC:

3643

AN:

26136

East Asian (EAS)

AF:

0.291

AC:

11555

AN:

39698

South Asian (SAS)

AF:

0.187

AC:

16165

AN:

86258

European-Finnish (FIN)

AF:

0.146

AC:

7807

AN:

53418

Middle Eastern (MID)

AF:

0.218

AC:

1257

AN:

5768

European-Non Finnish (NFE)

AF:

0.149

AC:

166029

AN:

1111946

Other (OTH)

AF:

0.202

AC:

12204

AN:

60394

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.488

Heterozygous variant carriers

12244

24488

36731

48975

61219

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

6300

12600

18900

25200

31500

<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:

0.310

AC:

47147

AN:

152094

Hom.:

11352

Cov.:

AF XY:

0.307

AC XY:

22864

AN XY:

74382

show subpopulations

African (AFR)

AF:

0.676

AC:

28026

AN:

41450

American (AMR)

AF:

0.241

AC:

3679

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.140

AC:

485

AN:

3470

East Asian (EAS)

AF:

0.269

AC:

1391

AN:

5170

South Asian (SAS)

AF:

0.193

AC:

929

AN:

4824

European-Finnish (FIN)

AF:

0.148

AC:

1570

AN:

10586

Middle Eastern (MID)

AF:

0.204

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.150

AC:

10169

AN:

67986

Other (OTH)

AF:

0.282

AC:

595

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1274

2548

3823

5097

6371

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

416

832

1248

1664

2080

<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:

0.199

Hom.:

21336

Bravo

AF:

0.337

Asia WGS

AF:

0.264

AC:

921

AN:

3478

EpiCase

AF:

0.157

EpiControl

AF:

0.160

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.68

CADD

Benign

6.1

(source)

DANN

Benign

0.57

PhyloP100

-0.96

Mutation Taster

=98/2

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

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