rs1718125

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_002562.6(P2RX7):​c.294+263C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 1,426,432 control chromosomes in the GnomAD database, including 16,847 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 0.19 ( 3457 hom., cov: 32)
Exomes 𝑓: 0.13 ( 13390 hom. )

Consequence

P2RX7
NM_002562.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.389

Publications

19 publications found
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.331 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
P2RX7NM_002562.6 linkc.294+263C>T intron_variant Intron 2 of 12 ENST00000328963.10 NP_002553.3 Q99572-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
P2RX7ENST00000328963.10 linkc.294+263C>T intron_variant Intron 2 of 12 1 NM_002562.6 ENSP00000330696.6 Q99572-1

Frequencies

GnomAD3 genomes
AF:
0.189
AC:
28714
AN:
151924
Hom.:
3449
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.335
Gnomad AMI
AF:
0.105
Gnomad AMR
AF:
0.0949
Gnomad ASJ
AF:
0.0732
Gnomad EAS
AF:
0.320
Gnomad SAS
AF:
0.231
Gnomad FIN
AF:
0.158
Gnomad MID
AF:
0.0823
Gnomad NFE
AF:
0.122
Gnomad OTH
AF:
0.150
GnomAD2 exomes
AF:
0.152
AC:
20159
AN:
132418
AF XY:
0.157
show subpopulations
Gnomad AFR exome
AF:
0.348
Gnomad AMR exome
AF:
0.0762
Gnomad ASJ exome
AF:
0.0751
Gnomad EAS exome
AF:
0.322
Gnomad FIN exome
AF:
0.154
Gnomad NFE exome
AF:
0.117
Gnomad OTH exome
AF:
0.123
GnomAD4 exome
AF:
0.135
AC:
171535
AN:
1274390
Hom.:
13390
Cov.:
32
AF XY:
0.136
AC XY:
85463
AN XY:
627134
show subpopulations
African (AFR)
AF:
0.351
AC:
10269
AN:
29238
American (AMR)
AF:
0.0757
AC:
2440
AN:
32224
Ashkenazi Jewish (ASJ)
AF:
0.0753
AC:
1639
AN:
21776
East Asian (EAS)
AF:
0.306
AC:
7782
AN:
25432
South Asian (SAS)
AF:
0.217
AC:
16812
AN:
77430
European-Finnish (FIN)
AF:
0.156
AC:
3594
AN:
22980
Middle Eastern (MID)
AF:
0.102
AC:
525
AN:
5150
European-Non Finnish (NFE)
AF:
0.120
AC:
120758
AN:
1009164
Other (OTH)
AF:
0.151
AC:
7716
AN:
50996
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.470
Heterozygous variant carriers
0
6781
13562
20343
27124
33905
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Exome Hom
Variant carriers
0
4888
9776
14664
19552
24440
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
AF:
0.189
AC:
28764
AN:
152042
Hom.:
3457
Cov.:
32
AF XY:
0.189
AC XY:
14032
AN XY:
74332
show subpopulations
African (AFR)
AF:
0.335
AC:
13886
AN:
41430
American (AMR)
AF:
0.0955
AC:
1459
AN:
15270
Ashkenazi Jewish (ASJ)
AF:
0.0732
AC:
254
AN:
3470
East Asian (EAS)
AF:
0.318
AC:
1644
AN:
5162
South Asian (SAS)
AF:
0.232
AC:
1120
AN:
4830
European-Finnish (FIN)
AF:
0.158
AC:
1667
AN:
10560
Middle Eastern (MID)
AF:
0.0952
AC:
28
AN:
294
European-Non Finnish (NFE)
AF:
0.122
AC:
8284
AN:
68000
Other (OTH)
AF:
0.154
AC:
326
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1114
2227
3341
4454
5568
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
304
608
912
1216
1520
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.135
Hom.:
3424
Bravo
AF:
0.188
Asia WGS
AF:
0.273
AC:
946
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.80
CADD
Benign
11
DANN
Benign
0.66
PhyloP100
0.39
Mutation Taster
=100/0
polymorphism (auto)

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.030
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs1718125; hg19: chr12-121593019; API