NM_002562.6:c.533+206C>A

Variant names:

• chr12-121162726-C-A
• rs1186055
• NM_002562.6:c.533+206C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002562.6(P2RX7):​c.533+206C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.358 in 151,932 control chromosomes in the GnomAD database, including 11,032 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 0.36 (11032 hom., cov: 30)
• Consequence: P2RX7 NM_002562.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.122
• Publications: 10 publications found

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]

ENSG00000295862 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.548 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
P2RX7	NM_002562.6	c.533+206C>A		intron_variant	Intron 5 of 12	ENST00000328963.10	NP_002553.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
P2RX7	ENST00000328963.10	c.533+206C>A		intron_variant	Intron 5 of 12	1	NM_002562.6	ENSP00000330696.6

Frequencies

GnomAD3 genomes AF: 0.358 AC: 54318 AN: 151814 Hom.: 10988 Cov.: 30

Gnomad AFR AF: 0.554

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.353

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.291

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.358 AC: 54435 AN: 151932 Hom.: 11032 Cov.: 30 AF XY: 0.356 AC XY: 26436 AN XY: 74282

African (AFR) AF: 0.554 AC: 22932 AN: 41400

American (AMR) AF: 0.283 AC: 4318 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.211 AC: 731 AN: 3466

East Asian (EAS) AF: 0.353 AC: 1817 AN: 5150

South Asian (SAS) AF: 0.331 AC: 1596 AN: 4828

European-Finnish (FIN) AF: 0.337 AC: 3561 AN: 10554

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.273 AC: 18540 AN: 67962

Other (OTH) AF: 0.294 AC: 619 AN: 2104

Alfa AF: 0.278 Hom.: 10485

Bravo AF: 0.362

Asia WGS AF: 0.358 AC: 1246 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.54
DANN	Benign	0.41
PhyloP100		-0.12
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1186055; hg19: chr12-121600529;