Variant 11-73234975-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_002564.4(P2RY2):c.816C>T(p.Arg272Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.551 in 1,609,496 control chromosomes in the GnomAD database, including 245,662 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 0.56 ( 24286 hom., cov: 34)

Exomes 𝑓: 0.55 ( 221376 hom. )

Consequence

P2RY2
NM_002564.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.251

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 -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.64).

BP7

Synonymous conserved (PhyloP=-0.251 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.626 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
P2RY2	NM_002564.4 linkuse as main transcript	c.816C>T	p.Arg272Arg	synonymous_variant	3/3	ENST00000393597.7	NP_002555.4	P41231
P2RY2	NM_176071.3 linkuse as main transcript	c.816C>T	p.Arg272Arg	synonymous_variant	3/3		NP_788085.3	P41231
P2RY2	NM_176072.3 linkuse as main transcript	c.816C>T	p.Arg272Arg	synonymous_variant	3/3		NP_788086.3	P41231

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
P2RY2	ENST00000393597.7 linkuse as main transcript	c.816C>T	p.Arg272Arg	synonymous_variant	3/3	1	NM_002564.4	ENSP00000377222.2	P41231
P2RY2	ENST00000311131.6 linkuse as main transcript	c.816C>T	p.Arg272Arg	synonymous_variant	3/3	1		ENSP00000310305.2	P41231
P2RY2	ENST00000393596.2 linkuse as main transcript	c.816C>T	p.Arg272Arg	synonymous_variant	3/3	1		ENSP00000377221.2	P41231

Frequencies

GnomAD3 genomes

AF:

0.564

AC:

85783

AN:

152050

Hom.:

24266

Cov.:

show subpopulations

Gnomad AFR

AF:

0.568

Gnomad AMI

AF:

0.401

Gnomad AMR

AF:

0.636

Gnomad ASJ

AF:

0.593

Gnomad EAS

AF:

0.642

Gnomad SAS

AF:

0.480

Gnomad FIN

AF:

0.557

Gnomad MID

AF:

0.611

Gnomad NFE

AF:

0.547

Gnomad OTH

AF:

0.584

GnomAD3 exomes

AF:

0.566

AC:

140698

AN:

248494

Hom.:

40341

AF XY:

0.558

AC XY:

75094

AN XY:

134594

show subpopulations

Gnomad AFR exome

AF:

0.565

Gnomad AMR exome

AF:

0.657

Gnomad ASJ exome

AF:

0.604

Gnomad EAS exome

AF:

0.649

Gnomad SAS exome

AF:

0.481

Gnomad FIN exome

AF:

0.556

Gnomad NFE exome

AF:

0.547

Gnomad OTH exome

AF:

0.560

GnomAD4 exome

AF:

0.550

AC:

800979

AN:

1457328

Hom.:

221376

Cov.:

AF XY:

0.547

AC XY:

397042

AN XY:

725204

show subpopulations

Gnomad4 AFR exome

AF:

0.571

Gnomad4 AMR exome

AF:

0.654

Gnomad4 ASJ exome

AF:

0.594

Gnomad4 EAS exome

AF:

0.621

Gnomad4 SAS exome

AF:

0.481

Gnomad4 FIN exome

AF:

0.554

Gnomad4 NFE exome

AF:

0.546

Gnomad4 OTH exome

AF:

0.560

GnomAD4 genome

AF:

0.564

AC:

85861

AN:

152168

Hom.:

24286

Cov.:

AF XY:

0.563

AC XY:

41908

AN XY:

74400

show subpopulations

Gnomad4 AFR

AF:

0.568

Gnomad4 AMR

AF:

0.636

Gnomad4 ASJ

AF:

0.593

Gnomad4 EAS

AF:

0.642

Gnomad4 SAS

AF:

0.481

Gnomad4 FIN

AF:

0.557

Gnomad4 NFE

AF:

0.547

Gnomad4 OTH

AF:

0.582

Alfa

AF:

0.555

Hom.:

42294

Bravo

AF:

0.575

Asia WGS

AF:

0.559

AC:

1946

AN:

3478

EpiCase

AF:

0.551

EpiControl

AF:

0.550

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.64

CADD

Benign

6.2

DANN

Benign

0.85

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over