Variant 17-3690982-TGG-TG details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_002561.4(P2RX5):c.333del(p.Asn112ThrfsTer36) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★). Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: 𝑓 0.58 ( 28350 hom., cov: 0)

Exomes 𝑓: 0.68 ( 345742 hom. )

Consequence

P2RX5
NM_002561.4 frameshift

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0370

Variant links:

Genes affected

P2RX5 (HGNC:8536): (purinergic receptor P2X 5) The product of this gene belongs to the family of purinoceptors for ATP. This receptor functions as a ligand-gated ion channel. Alternative splicing results in multiple transcript variants. Read-through transcription also exists between this gene and the neighboring downstream gene, TAX1BP3 (Tax1 binding protein 3). [provided by RefSeq, Mar 2011]

P2RX5 links:

P2RX5-TAX1BP3 (HGNC:):

P2RX5-TAX1BP3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 17-3690982-TG-T is Benign according to our data. Variant chr17-3690982-TG-T is described in ClinVar as [Benign]. Clinvar id is 403283.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.793 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
P2RX5	NM_002561.4 linkuse as main transcript	c.333del	p.Asn112ThrfsTer36	frameshift_variant	3/12	ENST00000225328.10
P2RX5-TAX1BP3	NR_037928.1 linkuse as main transcript	n.732del		non_coding_transcript_exon_variant	3/15

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
P2RX5	ENST00000225328.10 linkuse as main transcript	c.333del	p.Asn112ThrfsTer36	frameshift_variant	3/12	1	NM_002561.4		Q93086-3

Frequencies

GnomAD3 genomes

AF:

0.577

AC:

87617

AN:

151856

Hom.:

28342

Cov.:

show subpopulations

Gnomad AFR

AF:

0.261

Gnomad AMI

AF:

0.544

Gnomad AMR

AF:

0.716

Gnomad ASJ

AF:

0.583

Gnomad EAS

AF:

0.814

Gnomad SAS

AF:

0.596

Gnomad FIN

AF:

0.725

Gnomad MID

AF:

0.570

Gnomad NFE

AF:

0.696

Gnomad OTH

AF:

0.578

GnomAD3 exomes

AF:

0.676

AC:

167917

AN:

248528

Hom.:

59118

AF XY:

0.673

AC XY:

90610

AN XY:

134644

show subpopulations

Gnomad AFR exome

AF:

0.247

Gnomad AMR exome

AF:

0.807

Gnomad ASJ exome

AF:

0.584

Gnomad EAS exome

AF:

0.813

Gnomad SAS exome

AF:

0.600

Gnomad FIN exome

AF:

0.726

Gnomad NFE exome

AF:

0.694

Gnomad OTH exome

AF:

0.658

GnomAD4 exome

AF:

0.682

AC:

996324

AN:

1459892

Hom.:

345742

Cov.:

AF XY:

0.680

AC XY:

494003

AN XY:

726174

show subpopulations

Gnomad4 AFR exome

AF:

0.238

Gnomad4 AMR exome

AF:

0.793

Gnomad4 ASJ exome

AF:

0.582

Gnomad4 EAS exome

AF:

0.811

Gnomad4 SAS exome

AF:

0.603

Gnomad4 FIN exome

AF:

0.727

Gnomad4 NFE exome

AF:

0.696

Gnomad4 OTH exome

AF:

0.653

GnomAD4 genome

AF:

0.577

AC:

87654

AN:

151974

Hom.:

28350

Cov.:

AF XY:

0.581

AC XY:

43137

AN XY:

74280

show subpopulations

Gnomad4 AFR

AF:

0.261

Gnomad4 AMR

AF:

0.716

Gnomad4 ASJ

AF:

0.583

Gnomad4 EAS

AF:

0.814

Gnomad4 SAS

AF:

0.598

Gnomad4 FIN

AF:

0.725

Gnomad4 NFE

AF:

0.696

Gnomad4 OTH

AF:

0.579

Alfa

AF:

0.571

Hom.:

3610

Bravo

AF:

0.563

Asia WGS

AF:

0.639

AC:

2218

AN:

3476

EpiCase

AF:

0.679

EpiControl

AF:

0.678

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 28, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency in ESP (all): 6808/12518=54.38% -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

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