rs10898909

chr11-73241451-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.*6158G>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 0.213 in 152,542 control chromosomes in the GnomAD database, including 4,496 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 0.21 (4479 hom., cov: 33)
  • Exomes 𝑓: 0.29 (17 hom.)
• Consequence: P2RY2 NM_002564.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.245

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.495 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
P2RY2	NM_002564.4	c.*6158G>A		3_prime_UTR_variant	3/3	ENST00000393597.7
P2RY2	NM_176071.3	c.*6158G>A		3_prime_UTR_variant	3/3
P2RY2	NM_176072.3	c.*6158G>A		3_prime_UTR_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
P2RY2	ENST00000393597.7	c.*6158G>A		3_prime_UTR_variant	3/3	1	NM_002564.4	P1
	ENST00000565433.1	n.2477G>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.213 AC: 32325 AN: 152060 Hom.: 4468 Cov.: 33

Gnomad AFR AF: 0.0533

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.511

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.214

GnomAD4 exome AF: 0.286 AC: 104 AN: 364 Hom.: 17 Cov.: 0 AF XY: 0.270 AC XY: 48 AN XY: 178

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.250

Gnomad4 EAS exome AF: 0.452

Gnomad4 SAS exome AF: 0.250

Gnomad4 FIN exome AF: 0.293

Gnomad4 NFE exome AF: 0.262

Gnomad4 OTH exome AF: 0.308

GnomAD4 genome AF: 0.213 AC: 32351 AN: 152178 Hom.: 4479 Cov.: 33 AF XY: 0.216 AC XY: 16076 AN XY: 74386

Gnomad4 AFR AF: 0.0533

Gnomad4 AMR AF: 0.356

Gnomad4 ASJ AF: 0.169

Gnomad4 EAS AF: 0.511

Gnomad4 SAS AF: 0.223

Gnomad4 FIN AF: 0.256

Gnomad4 NFE AF: 0.250

Gnomad4 OTH AF: 0.215

Alfa AF: 0.239 Hom.: 6531

Bravo AF: 0.217

Asia WGS AF: 0.338 AC: 1175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.66
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10898909; hg19: chr11-72952496;