Variant chr11-73234209-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -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. 15/21 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

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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 id is 2642132.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 10 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
P2RY2	NM_002564.4 linkuse as main transcript	c.50A>G	p.Asp17Gly	missense_variant	3/3	ENST00000393597.7
P2RY2	NM_176071.3 linkuse as main transcript	c.50A>G	p.Asp17Gly	missense_variant	3/3
P2RY2	NM_176072.3 linkuse as main transcript	c.50A>G	p.Asp17Gly	missense_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris
P2RY2	ENST00000393597.7 linkuse as main transcript	c.50A>G	p.Asp17Gly	missense_variant	3/3	1	NM_002564.4	P1
P2RY2	ENST00000311131.6 linkuse as main transcript	c.50A>G	p.Asp17Gly	missense_variant	3/3	1		P1
P2RY2	ENST00000393596.2 linkuse as main transcript	c.50A>G	p.Asp17Gly	missense_variant	3/3	1		P1

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

GnomAD3 exomes

AF:

0.00519

AC:

1304

AN:

251038

Hom.:

AF XY:

0.00507

AC XY:

688

AN XY:

135656

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 SAS exome

AF:

0.00118

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

Gnomad4 AFR exome

AF:

0.000687

Gnomad4 AMR exome

AF:

0.00177

Gnomad4 ASJ exome

AF:

0.0298

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00147

Gnomad4 FIN exome

AF:

0.00768

Gnomad4 NFE exome

AF:

0.00620

Gnomad4 OTH exome

AF:

0.00659

GnomAD4 genome

AF:

0.00549

AC:

836

AN:

152160

Hom.:

Cov.:

AF XY:

0.00531

AC XY:

395

AN XY:

74400

show subpopulations

Gnomad4 AFR

AF:

0.000867

Gnomad4 AMR

AF:

0.00347

Gnomad4 ASJ

AF:

0.0357

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00104

Gnomad4 FIN

AF:

0.00699

Gnomad4 NFE

AF:

0.00791

Gnomad4 OTH

AF:

0.00284

Alfa

AF:

0.00759

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

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jan 01, 2023

P2RY2: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.066

BayesDel_addAF

Benign

-0.58

BayesDel_noAF

Benign

-0.59

CADD

Benign

DANN

Benign

0.96

DEOGEN2

Benign

0.049

T;T;T

Eigen

Benign

-0.67

Eigen_PC

Benign

-0.60

FATHMM_MKL

Benign

0.14

LIST_S2

Benign

0.61

.;.;T

M_CAP

Benign

0.0045

MetaRNN

Benign

0.0034

T;T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

1.5

L;L;L

MutationTaster

Benign

1.0

N;N;N

PrimateAI

Benign

0.31

PROVEAN

Benign

-0.28

N;N;N

REVEL

Benign

0.035

Sift

Benign

0.33

T;T;T

Sift4G

Benign

0.082

T;T;T

Polyphen

0.0

B;B;B

Vest4

0.11

MVP

0.50

MPC

0.46

ClinPred

0.0056

GERP RS

1.0

Varity_R

0.071

gMVP

0.50

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over