Variant 17-3903370-T-A 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 ENST00000225538.4(P2RX1):c.606-27A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 1,613,218 control chromosomes in the GnomAD database, including 12,680 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). There are indicators that this mutation may affect the branch point..

Frequency

Genomes: 𝑓 0.17 ( 3013 hom., cov: 32)

Exomes 𝑓: 0.10 ( 9667 hom. )

Consequence

P2RX1
ENST00000225538.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.60

Variant links:

Genes affected

P2RX1 (HGNC:8533): (purinergic receptor P2X 1) The protein encoded by this gene belongs to the P2X family of G-protein-coupled receptors. These proteins can form homo-and heterotimers and function as ATP-gated ion channels and mediate rapid and selective permeability to cations. This protein is primarily localized to smooth muscle where binds ATP and mediates synaptic transmission between neurons and from neurons to smooth muscle and may being responsible for sympathetic vasoconstriction in small arteries, arterioles and vas deferens. Mouse studies suggest that this receptor is essential for normal male reproductive function. This protein may also be involved in promoting apoptosis. [provided by RefSeq, Jun 2013]

P2RX1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

This place is a probable branch point but likely benign (scored 1 / 10). Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BP6

Variant 17-3903370-T-A is Benign according to our data. Variant chr17-3903370-T-A is described in ClinVar as [Benign]. Clinvar id is 1248529.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
P2RX1	NM_002558.4 linkuse as main transcript	c.606-27A>T		intron_variant		ENST00000225538.4	NP_002549.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
P2RX1	ENST00000225538.4 linkuse as main transcript	c.606-27A>T		intron_variant		1	NM_002558.4	ENSP00000225538	P1
P2RX1	ENST00000572418.1 linkuse as main transcript	n.1129-27A>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes

AF:

0.167

AC:

25321

AN:

152072

Hom.:

3004

Cov.:

show subpopulations

Gnomad AFR

AF:

0.331

Gnomad AMI

AF:

0.0637

Gnomad AMR

AF:

0.122

Gnomad ASJ

AF:

0.0877

Gnomad EAS

AF:

0.126

Gnomad SAS

AF:

0.196

Gnomad FIN

AF:

0.130

Gnomad MID

AF:

0.165

Gnomad NFE

AF:

0.0892

Gnomad OTH

AF:

0.153

GnomAD3 exomes

AF:

0.131

AC:

32660

AN:

249824

Hom.:

2745

AF XY:

0.130

AC XY:

17600

AN XY:

135116

show subpopulations

Gnomad AFR exome

AF:

0.339

Gnomad AMR exome

AF:

0.131

Gnomad ASJ exome

AF:

0.0959

Gnomad EAS exome

AF:

0.123

Gnomad SAS exome

AF:

0.198

Gnomad FIN exome

AF:

0.122

Gnomad NFE exome

AF:

0.0891

Gnomad OTH exome

AF:

0.121

GnomAD4 exome

AF:

0.102

AC:

149101

AN:

1461028

Hom.:

9667

Cov.:

AF XY:

0.105

AC XY:

76235

AN XY:

726748

show subpopulations

Gnomad4 AFR exome

AF:

0.344

Gnomad4 AMR exome

AF:

0.129

Gnomad4 ASJ exome

AF:

0.0941

Gnomad4 EAS exome

AF:

0.0789

Gnomad4 SAS exome

AF:

0.199

Gnomad4 FIN exome

AF:

0.118

Gnomad4 NFE exome

AF:

0.0851

Gnomad4 OTH exome

AF:

0.118

GnomAD4 genome

AF:

0.167

AC:

25351

AN:

152190

Hom.:

3013

Cov.:

AF XY:

0.168

AC XY:

12474

AN XY:

74410

show subpopulations

Gnomad4 AFR

AF:

0.330

Gnomad4 AMR

AF:

0.122

Gnomad4 ASJ

AF:

0.0877

Gnomad4 EAS

AF:

0.125

Gnomad4 SAS

AF:

0.196

Gnomad4 FIN

AF:

0.130

Gnomad4 NFE

AF:

0.0892

Gnomad4 OTH

AF:

0.154

Alfa

AF:

0.124

Hom.:

305

Bravo

AF:

0.173

Asia WGS

AF:

0.180

AC:

625

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 12, 2018	- -
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

0.41

DANN

Benign

0.79

La Branchor

0.76

BranchPoint Hunter

1.0

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