Variant chr12-132618781-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_170682.4(P2RX2):c.-36T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 1,196,890 control chromosomes in the GnomAD database, including 9,071 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.090 ( 837 hom., cov: 29)

Exomes 𝑓: 0.12 ( 8234 hom. )

Consequence

P2RX2
NM_170682.4 5_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.465

Variant links:

Genes affected

P2RX2 (HGNC:15459): (purinergic receptor P2X 2) The product of this gene belongs to the family of purinoceptors for ATP. This receptor functions as a ligand-gated ion channel. Binding to ATP mediates synaptic transmission between neurons and from neurons to smooth muscle. Multiple transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Aug 2013]

P2RX2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BP6

Variant 12-132618781-T-C is Benign according to our data. Variant chr12-132618781-T-C is described in ClinVar as [Benign]. Clinvar id is 508567.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.2 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
P2RX2	NM_170682.4 linkuse as main transcript	c.-36T>C		5_prime_UTR_variant	1/11	ENST00000643471.2	NP_733782.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
P2RX2	ENST00000643471.2 linkuse as main transcript	c.-36T>C		5_prime_UTR_variant	1/11		NM_170682.4	ENSP00000494644	A2	Q9UBL9-1

Frequencies

GnomAD3 genomes

AF:

0.0904

AC:

13540

AN:

149772

Hom.:

837

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0204

Gnomad AMI

AF:

0.209

Gnomad AMR

AF:

0.0598

Gnomad ASJ

AF:

0.127

Gnomad EAS

AF:

0.211

Gnomad SAS

AF:

0.0936

Gnomad FIN

AF:

0.117

Gnomad MID

AF:

0.0742

Gnomad NFE

AF:

0.124

Gnomad OTH

AF:

0.0797

GnomAD3 exomes

AF:

0.108

AC:

697

AN:

6430

Hom.:

AF XY:

0.110

AC XY:

359

AN XY:

3262

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.0500

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.167

Gnomad SAS exome

AF:

0.0690

Gnomad FIN exome

AF:

0.111

Gnomad NFE exome

AF:

0.103

Gnomad OTH exome

AF:

0.161

GnomAD4 exome

AF:

0.122

AC:

127316

AN:

1047008

Hom.:

8234

Cov.:

AF XY:

0.121

AC XY:

60099

AN XY:

496372

show subpopulations

Gnomad4 AFR exome

AF:

0.0153

Gnomad4 AMR exome

AF:

0.0501

Gnomad4 ASJ exome

AF:

0.132

Gnomad4 EAS exome

AF:

0.220

Gnomad4 SAS exome

AF:

0.0836

Gnomad4 FIN exome

AF:

0.120

Gnomad4 NFE exome

AF:

0.123

Gnomad4 OTH exome

AF:

0.116

GnomAD4 genome

AF:

0.0903

AC:

13536

AN:

149882

Hom.:

837

Cov.:

AF XY:

0.0903

AC XY:

6607

AN XY:

73184

show subpopulations

Gnomad4 AFR

AF:

0.0203

Gnomad4 AMR

AF:

0.0598

Gnomad4 ASJ

AF:

0.127

Gnomad4 EAS

AF:

0.211

Gnomad4 SAS

AF:

0.0938

Gnomad4 FIN

AF:

0.117

Gnomad4 NFE

AF:

0.124

Gnomad4 OTH

AF:

0.0808

Alfa

AF:

0.108

Hom.:

120

Bravo

AF:

0.0842

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 09, 2017

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

7.5

DANN

Benign

0.30

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over