11-73238127-G-A

Position:

• chr11-73238127-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002564.4(P2RY2):​c.*2834G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 152,126 control chromosomes in the GnomAD database, including 9,264 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 0.32 (9264 hom., cov: 32)
• Consequence: P2RY2 NM_002564.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.475

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.462 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
P2RY2	NM_002564.4	c.*2834G>A		3_prime_UTR_variant	3/3	ENST00000393597.7	NP_002555.4
P2RY2	NM_176071.3	c.*2834G>A		3_prime_UTR_variant	3/3		NP_788085.3
P2RY2	NM_176072.3	c.*2834G>A		3_prime_UTR_variant	3/3		NP_788086.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
P2RY2	ENST00000393597.7	c.*2834G>A		3_prime_UTR_variant	3/3	1	NM_002564.4	ENSP00000377222.2

Frequencies

GnomAD3 genomes AF: 0.319 AC: 48563 AN: 152008 Hom.: 9267 Cov.: 32

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.544

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.417

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.332

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.319 AC: 48562 AN: 152126 Hom.: 9264 Cov.: 32 AF XY: 0.324 AC XY: 24129 AN XY: 74372

Gnomad4 AFR AF: 0.101

Gnomad4 AMR AF: 0.359

Gnomad4 ASJ AF: 0.378

Gnomad4 EAS AF: 0.277

Gnomad4 SAS AF: 0.478

Gnomad4 FIN AF: 0.417

Gnomad4 NFE AF: 0.414

Gnomad4 OTH AF: 0.334

Alfa AF: 0.377 Hom.: 9859

Bravo AF: 0.302

Asia WGS AF: 0.354 AC: 1233 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	5.3
DANN	Benign	0.83

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs4944832; hg19: chr11-72949172;