rs2230912

chr12-121184393-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002562.6(P2RX7):c.1379A>G(p.Gln460Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 1,613,940 control chromosomes in the GnomAD database, including 20,186 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

• Frequency:
  • Genomes: 𝑓 0.12 (1306 hom., cov: 32)
  • Exomes 𝑓: 0.16 (18880 hom.)
• Consequence: P2RX7 NM_002562.6 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.30

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.0016370714).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.165 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
P2RX7	NM_002562.6	c.1379A>G	p.Gln460Arg	missense_variant	13/13	ENST00000328963.10
LOC105370032	XR_001749352.3	n.327+19105T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
P2RX7	ENST00000328963.10	c.1379A>G	p.Gln460Arg	missense_variant	13/13	1	NM_002562.6	P1
	ENST00000652651.1	n.3548+1808T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17985 AN: 152014 Hom.: 1308 Cov.: 32

Gnomad AFR AF: 0.0492

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.0799

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.114

GnomAD3 exomes AF: 0.130 AC: 32655 AN: 251306 Hom.: 2555 AF XY: 0.138 AC XY: 18692 AN XY: 135828

Gnomad AFR exome AF: 0.0514

Gnomad AMR exome AF: 0.0581

Gnomad ASJ exome AF: 0.167

Gnomad EAS exome AF: 0.000435

Gnomad SAS exome AF: 0.161

Gnomad FIN exome AF: 0.163

Gnomad NFE exome AF: 0.166

Gnomad OTH exome AF: 0.130

GnomAD4 exome AF: 0.156 AC: 227374 AN: 1461808 Hom.: 18880 Cov.: 34 AF XY: 0.156 AC XY: 113436 AN XY: 727206

Gnomad4 AFR exome AF: 0.0501

Gnomad4 AMR exome AF: 0.0608

Gnomad4 ASJ exome AF: 0.170

Gnomad4 EAS exome AF: 0.000453

Gnomad4 SAS exome AF: 0.163

Gnomad4 FIN exome AF: 0.157

Gnomad4 NFE exome AF: 0.168

Gnomad4 OTH exome AF: 0.144

GnomAD4 genome AF: 0.118 AC: 17987 AN: 152132 Hom.: 1306 Cov.: 32 AF XY: 0.116 AC XY: 8659 AN XY: 74354

Gnomad4 AFR AF: 0.0493

Gnomad4 AMR AF: 0.0798

Gnomad4 ASJ AF: 0.165

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.162

Gnomad4 NFE AF: 0.167

Gnomad4 OTH AF: 0.112

Alfa AF: 0.156 Hom.: 4895

Bravo AF: 0.108

TwinsUK AF: 0.167 AC: 621

ALSPAC AF: 0.164 AC: 633

ESP6500AA AF: 0.0527 AC: 232

ESP6500EA AF: 0.166 AC: 1429

ExAC AF: 0.132 AC: 15978

Asia WGS AF: 0.0640 AC: 224 AN: 3478

EpiCase AF: 0.169

EpiControl AF: 0.164

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.081
BayesDel_addAF	Benign	-0.32	T
BayesDel_noAF	Benign	-0.090
Cadd	Benign	16
Dann	Benign	0.87
DEOGEN2	Benign	0.13	T
Eigen	Benign	-0.23
Eigen_PC	Benign	-0.13
FATHMM_MKL	Benign	0.65	D
LIST_S2	Benign	0.56	T
MetaRNN	Benign	0.0016	T
MetaSVM	Benign	-0.90	T
MutationAssessor	Uncertain	2.2	M
MutationTaster	Benign	0.95	P;P;P;P
PrimateAI	Benign	0.32	T
REVEL	Benign	0.22
Sift4G	Benign	0.41	T
Polyphen		0.0030	B
Vest4		0.021
ClinPred		0.011	T
GERP RS		5.2
Varity_R		0.065
gMVP		0.24

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: rs2230912; hg19: chr12-121622196; COSMIC: COSV55854311;