Variant 17-3897786-C-T 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_002558.4(P2RX1):c.*28G>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 0.332 in 1,605,494 control chromosomes in the GnomAD database, including 94,566 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.28 ( 6801 hom., cov: 31)

Exomes 𝑓: 0.34 ( 87765 hom. )

Consequence

P2RX1
NM_002558.4 3_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.80

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

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP6

Variant 17-3897786-C-T is Benign according to our data. Variant chr17-3897786-C-T is described in ClinVar as [Benign]. Clinvar id is 1268219.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.358 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
P2RX1	NM_002558.4 link	c.*28G>A		3_prime_UTR_variant	12/12	ENST00000225538.4	NP_002549.1	P51575

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
P2RX1	ENST00000225538 link	c.*28G>A		3_prime_UTR_variant	12/12	1	NM_002558.4	ENSP00000225538.3		P51575
P2RX1	ENST00000572418.1 link	n.1751G>A		non_coding_transcript_exon_variant	11/11	2

Frequencies

GnomAD3 genomes

AF:

0.285

AC:

43259

AN:

151954

Hom.:

6802

Cov.:

show subpopulations

Gnomad AFR

AF:

0.213

Gnomad AMI

AF:

0.415

Gnomad AMR

AF:

0.218

Gnomad ASJ

AF:

0.295

Gnomad EAS

AF:

0.0721

Gnomad SAS

AF:

0.141

Gnomad FIN

AF:

0.326

Gnomad MID

AF:

0.231

Gnomad NFE

AF:

0.362

Gnomad OTH

AF:

0.274

GnomAD3 exomes

AF:

0.268

AC:

66063

AN:

246436

Hom.:

10241

AF XY:

0.270

AC XY:

36057

AN XY:

133470

show subpopulations

Gnomad AFR exome

AF:

0.211

Gnomad AMR exome

AF:

0.142

Gnomad ASJ exome

AF:

0.301

Gnomad EAS exome

AF:

0.0709

Gnomad SAS exome

AF:

0.159

Gnomad FIN exome

AF:

0.323

Gnomad NFE exome

AF:

0.363

Gnomad OTH exome

AF:

0.284

GnomAD4 exome

AF:

0.337

AC:

489534

AN:

1453422

Hom.:

87765

Cov.:

AF XY:

0.332

AC XY:

239833

AN XY:

723342

show subpopulations

Gnomad4 AFR exome

AF:

0.212

Gnomad4 AMR exome

AF:

0.151

Gnomad4 ASJ exome

AF:

0.304

Gnomad4 EAS exome

AF:

0.0620

Gnomad4 SAS exome

AF:

0.162

Gnomad4 FIN exome

AF:

0.328

Gnomad4 NFE exome

AF:

0.374

Gnomad4 OTH exome

AF:

0.318

GnomAD4 genome

AF:

0.284

AC:

43262

AN:

152072

Hom.:

6801

Cov.:

AF XY:

0.276

AC XY:

20546

AN XY:

74328

show subpopulations

Gnomad4 AFR

AF:

0.213

Gnomad4 AMR

AF:

0.218

Gnomad4 ASJ

AF:

0.295

Gnomad4 EAS

AF:

0.0719

Gnomad4 SAS

AF:

0.141

Gnomad4 FIN

AF:

0.326

Gnomad4 NFE

AF:

0.362

Gnomad4 OTH

AF:

0.270

Alfa

AF:

0.333

Hom.:

8900

Bravo

AF:

0.276

Asia WGS

AF:

0.0960

AC:

334

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

-0.89

CADD

Benign

0.61

DANN

Benign

0.60

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.070

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