dbSNP rs4382936: P2RY2:c.*6062A>C (chr11-73241355-A-C) – 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.*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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.428

Publications

13 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=-0.94).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.662 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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
P2RY2	NM_002564.4	MANE Select	c.*6062A>C	3_prime_UTR	Exon 3 of 3	NP_002555.4
P2RY2	NM_176071.3		c.*6062A>C	3_prime_UTR	Exon 3 of 3	NP_788085.3	P41231
P2RY2	NM_176072.3		c.*6062A>C	3_prime_UTR	Exon 3 of 3	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.*6062A>C		3_prime_UTR	Exon 3 of 3	ENSP00000377222.2	P41231
	ENSG00000260401	ENST00000565433.1	TSL:6	n.2381A>C		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.360

AC:

54736

AN:

152032

Hom.:

10510

Cov.:

show subpopulations

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:

AN:

196

Hom.:

Cov.:

AF XY:

0.310

AC XY:

AN XY:

116

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.750

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.500

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.611

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.299

AC:

AN:

134

Other (OTH)

AF:

0.333

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.491

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

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:

0.360

AC:

54827

AN:

152150

Hom.:

10539

Cov.:

AF XY:

0.365

AC XY:

27169

AN XY:

74378

show subpopulations

African (AFR)

AF:

0.282

AC:

11709

AN:

41520

American (AMR)

AF:

0.497

AC:

7589

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.244

AC:

847

AN:

3472

East Asian (EAS)

AF:

0.681

AC:

3521

AN:

5170

South Asian (SAS)

AF:

0.331

AC:

1600

AN:

4828

European-Finnish (FIN)

AF:

0.402

AC:

4243

AN:

10566

Middle Eastern (MID)

AF:

0.272

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.354

AC:

24060

AN:

67990

Other (OTH)

AF:

0.351

AC:

742

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.511

Heterozygous variant carriers

1834

3668

5502

7336

9170

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

520

1040

1560

2080

2600

<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:

0.350

Hom.:

17790

Bravo

AF:

0.366

Asia WGS

AF:

0.507

AC:

1761

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

4.1

(source)

DANN

Benign

0.50

PhyloP100

0.43

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over