rs3751142

Positions:

• chr12-121184616-G-T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_002562.6(P2RX7):​c.1602G>T​(p.Leu534=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0969 in 1,611,842 control chromosomes in the GnomAD database, including 10,317 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.12 (1446 hom., cov: 33)
  • Exomes 𝑓: 0.094 (8871 hom.)
• Consequence: P2RX7 NM_002562.6 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.00

Genes affected

P2RX7 (HGNC:8537): (purinergic receptor P2X 7) The product of this gene belongs to the family of purinoceptors for ATP. This receptor functions as a ligand-gated ion channel and is responsible for ATP-dependent lysis of macrophages through the formation of membrane pores permeable to large molecules. Activation of this nuclear receptor by ATP in the cytoplasm may be a mechanism by which cellular activity can be coupled to changes in gene expression. Multiple alternatively spliced variants have been identified, most of which fit nonsense-mediated decay (NMD) criteria. [provided by RefSeq, Jul 2010]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BP7: Synonymous conserved (PhyloP=3 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
P2RX7	NM_002562.6	c.1602G>T	p.Leu534=	synonymous_variant	13/13	ENST00000328963.10
LOC105370032	XR_001749352.3	n.327+18882C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
P2RX7	ENST00000328963.10	c.1602G>T	p.Leu534=	synonymous_variant	13/13	1	NM_002562.6	P1
	ENST00000652651.1	n.3548+1585C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18641 AN: 152170 Hom.: 1434 Cov.: 33

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.0556

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0777

Gnomad OTH AF: 0.100

GnomAD3 exomes AF: 0.142 AC: 34790 AN: 244858 Hom.: 3771 AF XY: 0.133 AC XY: 17612 AN XY: 132822

Gnomad AFR exome AF: 0.160

Gnomad AMR exome AF: 0.360

Gnomad ASJ exome AF: 0.0589

Gnomad EAS exome AF: 0.175

Gnomad SAS exome AF: 0.156

Gnomad FIN exome AF: 0.126

Gnomad NFE exome AF: 0.0758

Gnomad OTH exome AF: 0.114

GnomAD4 exome AF: 0.0943 AC: 137569 AN: 1459554 Hom.: 8871 Cov.: 41 AF XY: 0.0940 AC XY: 68221 AN XY: 726014

Gnomad4 AFR exome AF: 0.154

Gnomad4 AMR exome AF: 0.338

Gnomad4 ASJ exome AF: 0.0602

Gnomad4 EAS exome AF: 0.156

Gnomad4 SAS exome AF: 0.150

Gnomad4 FIN exome AF: 0.127

Gnomad4 NFE exome AF: 0.0753

Gnomad4 OTH exome AF: 0.100

GnomAD4 genome AF: 0.123 AC: 18685 AN: 152288 Hom.: 1446 Cov.: 33 AF XY: 0.127 AC XY: 9428 AN XY: 74462

Gnomad4 AFR AF: 0.158

Gnomad4 AMR AF: 0.220

Gnomad4 ASJ AF: 0.0556

Gnomad4 EAS AF: 0.164

Gnomad4 SAS AF: 0.162

Gnomad4 FIN AF: 0.128

Gnomad4 NFE AF: 0.0777

Gnomad4 OTH AF: 0.106

Alfa AF: 0.0924 Hom.: 355

Bravo AF: 0.132

Asia WGS AF: 0.181 AC: 630 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	2.1
DANN	Benign	0.77

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

Other links and lift over

dbSNP: rs3751142; hg19: chr12-121622419; COSMIC: COSV55853273;