rs12497578

Positions:

• chr3-152838684-C-G

Variant summary

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

The NM_002563.5(P2RY1):​c.*1780C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0838 in 152,194 control chromosomes in the GnomAD database, including 647 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 0.084 (647 hom., cov: 32)
  • Exomes 𝑓: 0.17 (0 hom.)
• Consequence: P2RY1 NM_002563.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.505

Genes affected

P2RY1 (HGNC:8539): (purinergic receptor P2Y1) The product of this gene belongs to the family of 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 functions as a receptor for extracellular ATP and ADP. In platelets binding to ADP leads to mobilization of intracellular calcium ions via activation of phospholipase C, a change in platelet shape, and probably to platelet aggregation. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
P2RY1	NM_002563.5	c.*1780C>G		3_prime_UTR_variant	1/1	ENST00000305097.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
P2RY1	ENST00000305097.6	c.*1780C>G		3_prime_UTR_variant	1/1		NM_002563.5	P1

Frequencies

GnomAD3 genomes AF: 0.0839 AC: 12754 AN: 152070 Hom.: 648 Cov.: 32

Gnomad AFR AF: 0.0464

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.0818

Gnomad EAS AF: 0.234

Gnomad SAS AF: 0.0414

Gnomad FIN AF: 0.0663

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0959

Gnomad OTH AF: 0.0950

GnomAD4 exome AF: 0.167 AC: 1 AN: 6 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 4

Gnomad4 ASJ exome AF: 0.00

Gnomad4 NFE exome AF: 0.500

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0838 AC: 12755 AN: 152188 Hom.: 647 Cov.: 32 AF XY: 0.0837 AC XY: 6226 AN XY: 74418

Gnomad4 AFR AF: 0.0465

Gnomad4 AMR AF: 0.103

Gnomad4 ASJ AF: 0.0818

Gnomad4 EAS AF: 0.234

Gnomad4 SAS AF: 0.0412

Gnomad4 FIN AF: 0.0663

Gnomad4 NFE AF: 0.0959

Gnomad4 OTH AF: 0.0955

Alfa AF: 0.0874 Hom.: 82

Bravo AF: 0.0897

Asia WGS AF: 0.123 AC: 429 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	1.3
DANN	Benign	0.77

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

Other links and lift over

dbSNP: rs12497578; hg19: chr3-152556473;