Genetic Variant NM_002564.4:c.310G>A (chr11-73234469-G-A) – ACMG Classification: Uncertain_significance (1 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2BP4

The NM_002564.4(P2RY2):c.310G>A(p.Val104Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 34)

Consequence

P2RY2
NM_002564.4 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.98

Publications

1 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:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.33436164).

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.310G>A	p.Val104Met	missense	Exon 3 of 3	NP_002555.4
P2RY2	NM_176071.3		c.310G>A	p.Val104Met	missense	Exon 3 of 3	NP_788085.3	P41231
P2RY2	NM_176072.3		c.310G>A	p.Val104Met	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.310G>A	p.Val104Met	missense	Exon 3 of 3	ENSP00000377222.2	P41231
P2RY2	ENST00000311131.6	TSL:1	c.310G>A	p.Val104Met	missense	Exon 3 of 3	ENSP00000310305.2	P41231
P2RY2	ENST00000393596.2	TSL:1	c.310G>A	p.Val104Met	missense	Exon 3 of 3	ENSP00000377221.2	P41231

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Cov.:

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

ClinVar

ClinVar submissions

Significance:Uncertain significance

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.13

BayesDel_addAF

Benign

-0.096

BayesDel_noAF

Benign

-0.38

CADD

Benign

(source)

DANN

Uncertain

1.0

DEOGEN2

Benign

0.080

Eigen

Benign

0.15

Eigen_PC

Benign

0.056

FATHMM_MKL

Benign

0.22

LIST_S2

Uncertain

0.95

M_CAP

Benign

0.066

MetaRNN

Benign

0.33

MetaSVM

Benign

-0.46

MutationAssessor

Benign

1.3

PhyloP100

2.0

PrimateAI

Uncertain

0.56

PROVEAN

Benign

-0.48

REVEL

Uncertain

0.32

Sift

Benign

0.20

Sift4G

Benign

0.23

Polyphen

0.77

Vest4

0.31

MutPred

0.57

Gain of catalytic residue at V104 (P = 0.01)

MVP

0.86

MPC

0.59

ClinPred

0.59

GERP RS

3.4

Varity_R

0.058

gMVP

0.21

Mutation Taster

=100/0

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over