rs1653625

Variant names:

• chr12-121185082-C-A
• rs1653625
• ENST00000261826.10:n.*1521C>A

Your query was ambiguous. Multiple possible variants found:

• chr12-121185082-C-A
• chr12-121185082-C-G

Variant summary

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

The ENST00000261826.10(P2RX7):​n.*1521C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.366 in 195,154 control chromosomes in the GnomAD database, including 12,502 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 0.44 (12092 hom., cov: 26)
  • Exomes 𝑓: 0.22 (410 hom.)
• Consequence: P2RX7 ENST00000261826.10 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.880
• Publications: 9 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]

ENSG00000286248 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.58 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000261826.10. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	P2RX7	NM_002562.6	MANE Select	c.*280C>A		3_prime_UTR	Exon 13 of 13	NP_002553.3
	P2RX7	NR_033948.2		n.2386C>A		non_coding_transcript_exon	Exon 13 of 13
	P2RX7	NR_033949.2		n.2302C>A		non_coding_transcript_exon	Exon 14 of 14

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	P2RX7	ENST00000261826.10	TSL:1	n.*1521C>A		non_coding_transcript_exon	Exon 12 of 12	ENSP00000261826.6
	P2RX7	ENST00000328963.10	TSL:1 MANE Select	c.*280C>A		3_prime_UTR	Exon 13 of 13	ENSP00000330696.6
	P2RX7	ENST00000261826.10	TSL:1	n.*1521C>A		3_prime_UTR	Exon 12 of 12	ENSP00000261826.6

Frequencies

GnomAD3 genomes AF: 0.435 AC: 57649 AN: 132502 Hom.: 12068 Cov.: 26

Gnomad AFR AF: 0.586

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.421

Gnomad MID AF: 0.300

Gnomad NFE AF: 0.360

Gnomad OTH AF: 0.394

GnomAD4 exome AF: 0.219 AC: 13687 AN: 62560 Hom.: 410 Cov.: 0 AF XY: 0.219 AC XY: 6978 AN XY: 31822

African (AFR) AF: 0.368 AC: 739 AN: 2008

American (AMR) AF: 0.277 AC: 641 AN: 2312

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 412 AN: 2306

East Asian (EAS) AF: 0.162 AC: 770 AN: 4752

South Asian (SAS) AF: 0.263 AC: 758 AN: 2886

European-Finnish (FIN) AF: 0.223 AC: 813 AN: 3650

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.214 AC: 8609 AN: 40304

Other (OTH) AF: 0.218 AC: 881 AN: 4048

GnomAD4 genome AF: 0.435 AC: 57727 AN: 132594 Hom.: 12092 Cov.: 26 AF XY: 0.434 AC XY: 27946 AN XY: 64324

African (AFR) AF: 0.586 AC: 23020 AN: 39288

American (AMR) AF: 0.413 AC: 5566 AN: 13488

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 799 AN: 2828

East Asian (EAS) AF: 0.298 AC: 1466 AN: 4924

South Asian (SAS) AF: 0.451 AC: 1871 AN: 4150

European-Finnish (FIN) AF: 0.421 AC: 3327 AN: 7912

Middle Eastern (MID) AF: 0.320 AC: 85 AN: 266

European-Non Finnish (NFE) AF: 0.360 AC: 20593 AN: 57184

Other (OTH) AF: 0.397 AC: 715 AN: 1802

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.74
DANN	Benign	0.33
PhyloP100		-0.88
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: rs1653625; hg19: chr12-121622885;