11-73233076-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002564.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	P2RY2	NM_002564.4	MANE Select	c.-4-1080C>T		intron	N/A	NP_002555.4
	P2RY2	NM_176071.3		c.-4-1080C>T		intron	N/A	NP_788085.3	P41231
	P2RY2	NM_176072.3		c.-138-946C>T		intron	N/A	NP_788086.3	P41231

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	P2RY2	ENST00000393597.7	TSL:1 MANE Select	c.-4-1080C>T		intron	N/A	ENSP00000377222.2	P41231
	P2RY2	ENST00000311131.6	TSL:1	c.-138-946C>T		intron	N/A	ENSP00000310305.2	P41231
	P2RY2	ENST00000393596.2	TSL:1	c.-4-1080C>T		intron	N/A	ENSP00000377221.2	P41231

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

African (AFR) AF: 0.563 AC: 23300 AN: 41364

American (AMR) AF: 0.938 AC: 14338 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.974 AC: 3381 AN: 3470

East Asian (EAS) AF: 1.00 AC: 5175 AN: 5176

South Asian (SAS) AF: 0.971 AC: 4675 AN: 4816

European-Finnish (FIN) AF: 0.983 AC: 10432 AN: 10614

Middle Eastern (MID) AF: 0.925 AC: 272 AN: 294

European-Non Finnish (NFE) AF: 0.955 AC: 64949 AN: 68008

Other (OTH) AF: 0.893 AC: 1886 AN: 2112

Alfa AF: 0.905 Hom.: 41672

Bravo AF: 0.835

Asia WGS AF: 0.963 AC: 3349 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.012
DANN	Benign	0.27
PhyloP100		-2.4
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1791926; hg19: chr11-72944121;