11-73233076-C-T

Variant names:

• chr11-73233076-C-T
• rs1791926
• NM_002564.4:c.-4-1080C>T

Variant summary

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

The NM_002564.4(P2RY2):​c.-4-1080C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.85 in 152,050 control chromosomes in the GnomAD database, including 57,392 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 0.85 (57392 hom., cov: 30)
• Consequence: P2RY2 NM_002564.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.40

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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
P2RY2	NM_002564.4	c.-4-1080C>T		intron_variant	Intron 2 of 2	ENST00000393597.7	NP_002555.4
P2RY2	NM_176071.3	c.-4-1080C>T		intron_variant	Intron 2 of 2		NP_788085.3
P2RY2	NM_176072.3	c.-138-946C>T		intron_variant	Intron 2 of 2		NP_788086.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
P2RY2	ENST00000393597.7	c.-4-1080C>T		intron_variant	Intron 2 of 2	1	NM_002564.4	ENSP00000377222.2
P2RY2	ENST00000311131.6	c.-138-946C>T		intron_variant	Intron 2 of 2	1		ENSP00000310305.2
P2RY2	ENST00000393596.2	c.-4-1080C>T		intron_variant	Intron 2 of 2	1		ENSP00000377221.2

Frequencies

GnomAD3 genomes AF: 0.851 AC: 129239 AN: 151932 Hom.: 57368 Cov.: 30

Gnomad AFR AF: 0.563

Gnomad AMI AF: 0.998

Gnomad AMR AF: 0.938

Gnomad ASJ AF: 0.974

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.970

Gnomad FIN AF: 0.983

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.955

Gnomad OTH AF: 0.892

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

GnomAD4 genome AF: 0.850 AC: 129318 AN: 152050 Hom.: 57392 Cov.: 30 AF XY: 0.856 AC XY: 63649 AN XY: 74354

Gnomad4 AFR AF: 0.563

Gnomad4 AMR AF: 0.938

Gnomad4 ASJ AF: 0.974

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.971

Gnomad4 FIN AF: 0.983

Gnomad4 NFE AF: 0.955

Gnomad4 OTH AF: 0.893

Alfa AF: 0.904 Hom.: 26434

Bravo AF: 0.835

Asia WGS AF: 0.963 AC: 3349 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.012
DANN	Benign	0.27

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: rs1791926; hg19: chr11-72944121;