dbSNP rs10898909: P2RY2:c.*6158G>A (chr11-73241451-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.245

Publications

14 publications found

Variant links:

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]

P2RY2 links:

ENSG00000260401 (HGNC:):

ENSG00000260401 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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	Effect	Exon rank	MANE	Protein	UniProt
P2RY2	NM_002564.4 link	c.*6158G>A	3_prime_UTR_variant	Exon 3 of 3	ENST00000393597.7	NP_002555.4	P41231
P2RY2	NM_176071.3 link	c.*6158G>A	3_prime_UTR_variant	Exon 3 of 3		NP_788085.3	P41231
P2RY2	NM_176072.3 link	c.*6158G>A	3_prime_UTR_variant	Exon 3 of 3		NP_788086.3	P41231

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
P2RY2	ENST00000393597.7 link	c.*6158G>A		3_prime_UTR_variant	Exon 3 of 3	1	NM_002564.4	ENSP00000377222.2		P41231
ENSG00000260401	ENST00000565433.1 link	n.2477G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes

AF:

0.213

AC:

32325

AN:

152060

Hom.:

4468

Cov.:

show subpopulations

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.:

Cov.:

AF XY:

0.270

AC XY:

AN XY:

178

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.250

AC:

AN:

East Asian (EAS)

AF:

0.452

AC:

AN:

South Asian (SAS)

AF:

0.250

AC:

AN:

European-Finnish (FIN)

AF:

0.293

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.262

AC:

AN:

214

Other (OTH)

AF:

0.308

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.519

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.213

AC:

32351

AN:

152178

Hom.:

4479

Cov.:

AF XY:

0.216

AC XY:

16076

AN XY:

74386

show subpopulations

African (AFR)

AF:

0.0533

AC:

2215

AN:

41540

American (AMR)

AF:

0.356

AC:

5445

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.169

AC:

585

AN:

3468

East Asian (EAS)

AF:

0.511

AC:

2640

AN:

5166

South Asian (SAS)

AF:

0.223

AC:

1074

AN:

4826

European-Finnish (FIN)

AF:

0.256

AC:

2711

AN:

10584

Middle Eastern (MID)

AF:

0.126

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.250

AC:

16964

AN:

67990

Other (OTH)

AF:

0.215

AC:

454

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1273

2546

3819

5092

6365

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

328

656

984

1312

1640

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.230

Hom.:

9908

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

(source)

DANN

Benign

0.48

PhyloP100

-0.24

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over