rs4382936

Positions:

• chr11-73241355-A-C
• chr11-73241355-A-T

Variant summary

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

The NM_002564.4(P2RY2):​c.*6062A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.36 in 152,346 control chromosomes in the GnomAD database, including 10,553 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 0.36 (10539 hom., cov: 33)
  • Exomes 𝑓: 0.33 (14 hom.)
• Consequence: P2RY2 NM_002564.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.428

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]

ENSG00000260401 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.662 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
P2RY2	NM_002564.4	c.*6062A>C		3_prime_UTR_variant	3/3	ENST00000393597.7	NP_002555.4
P2RY2	NM_176071.3	c.*6062A>C		3_prime_UTR_variant	3/3		NP_788085.3
P2RY2	NM_176072.3	c.*6062A>C		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.*6062A>C		3_prime_UTR_variant	3/3	1	NM_002564.4	ENSP00000377222.2
ENSG00000260401	ENST00000565433.1	n.2381A>C		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54736 AN: 152032 Hom.: 10510 Cov.: 33

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.681

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.354

Gnomad OTH AF: 0.351

GnomAD4 exome AF: 0.332 AC: 65 AN: 196 Hom.: 14 Cov.: 0 AF XY: 0.310 AC XY: 36 AN XY: 116

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.750

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.611

Gnomad4 NFE exome AF: 0.299

Gnomad4 OTH exome AF: 0.333

GnomAD4 genome AF: 0.360 AC: 54827 AN: 152150 Hom.: 10539 Cov.: 33 AF XY: 0.365 AC XY: 27169 AN XY: 74378

Gnomad4 AFR AF: 0.282

Gnomad4 AMR AF: 0.497

Gnomad4 ASJ AF: 0.244

Gnomad4 EAS AF: 0.681

Gnomad4 SAS AF: 0.331

Gnomad4 FIN AF: 0.402

Gnomad4 NFE AF: 0.354

Gnomad4 OTH AF: 0.351

Alfa AF: 0.345 Hom.: 12213

Bravo AF: 0.366

Asia WGS AF: 0.507 AC: 1761 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.1
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4382936; hg19: chr11-72952400;