Variant 17-3897729-G-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 NM_002558.4(P2RX1):c.*85C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0531 in 1,240,128 control chromosomes in the GnomAD database, including 1,996 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.042 ( 168 hom., cov: 32)

Exomes 𝑓: 0.055 ( 1828 hom. )

Consequence

P2RX1
NM_002558.4 3_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.482

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.73).

BP6

Variant 17-3897729-G-A is Benign according to our data. Variant chr17-3897729-G-A is described in ClinVar as [Benign]. Clinvar id is 1229012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0607 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
P2RX1	NM_002558.4 link	c.*85C>T		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.*85C>T		3_prime_UTR_variant	12/12	1	NM_002558.4	ENSP00000225538.3		P51575
P2RX1	ENST00000572418.1 link	n.1808C>T		non_coding_transcript_exon_variant	11/11	2

Frequencies

GnomAD3 genomes

AF:

0.0422

AC:

6424

AN:

152144

Hom.:

168

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0104

Gnomad AMI

AF:

0.0307

Gnomad AMR

AF:

0.0394

Gnomad ASJ

AF:

0.0611

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0318

Gnomad FIN

AF:

0.0623

Gnomad MID

AF:

0.0285

Gnomad NFE

AF:

0.0622

Gnomad OTH

AF:

0.0441

GnomAD4 exome

AF:

0.0546

AC:

59392

AN:

1087866

Hom.:

1828

Cov.:

AF XY:

0.0544

AC XY:

30113

AN XY:

553988

show subpopulations

Gnomad4 AFR exome

AF:

0.00931

Gnomad4 AMR exome

AF:

0.0302

Gnomad4 ASJ exome

AF:

0.0634

Gnomad4 EAS exome

AF:

0.0000562

Gnomad4 SAS exome

AF:

0.0360

Gnomad4 FIN exome

AF:

0.0618

Gnomad4 NFE exome

AF:

0.0610

Gnomad4 OTH exome

AF:

0.0511

GnomAD4 genome

AF:

0.0422

AC:

6423

AN:

152262

Hom.:

168

Cov.:

AF XY:

0.0431

AC XY:

3207

AN XY:

74440

show subpopulations

Gnomad4 AFR

AF:

0.0104

Gnomad4 AMR

AF:

0.0394

Gnomad4 ASJ

AF:

0.0611

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.0323

Gnomad4 FIN

AF:

0.0623

Gnomad4 NFE

AF:

0.0622

Gnomad4 OTH

AF:

0.0431

Alfa

AF:

0.0565

Hom.:

Bravo

AF:

0.0385

Asia WGS

AF:

0.0140

AC:

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	Jun 21, 2021	- -
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

-0.73

CADD

Benign

4.3

DANN

Benign

0.83

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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