12-121141854-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_002562.6(P2RX7):​c.125+8759C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 151,906 control chromosomes in the GnomAD database, including 6,323 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 0.27 ( 6323 hom., cov: 31)

Consequence

P2RX7
NM_002562.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.31
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 made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.407 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
P2RX7NM_002562.6 linkuse as main transcriptc.125+8759C>A intron_variant ENST00000328963.10
LOC105370032XR_001749352.3 linkuse as main transcriptn.328-15013G>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
P2RX7ENST00000328963.10 linkuse as main transcriptc.125+8759C>A intron_variant 1 NM_002562.6 P1Q99572-1

Frequencies

GnomAD3 genomes
AF:
0.269
AC:
40791
AN:
151788
Hom.:
6293
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.412
Gnomad AMI
AF:
0.137
Gnomad AMR
AF:
0.168
Gnomad ASJ
AF:
0.170
Gnomad EAS
AF:
0.314
Gnomad SAS
AF:
0.284
Gnomad FIN
AF:
0.309
Gnomad MID
AF:
0.101
Gnomad NFE
AF:
0.203
Gnomad OTH
AF:
0.220
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.269
AC:
40890
AN:
151906
Hom.:
6323
Cov.:
31
AF XY:
0.271
AC XY:
20085
AN XY:
74216
show subpopulations
Gnomad4 AFR
AF:
0.412
Gnomad4 AMR
AF:
0.168
Gnomad4 ASJ
AF:
0.170
Gnomad4 EAS
AF:
0.314
Gnomad4 SAS
AF:
0.287
Gnomad4 FIN
AF:
0.309
Gnomad4 NFE
AF:
0.203
Gnomad4 OTH
AF:
0.223
Alfa
AF:
0.195
Hom.:
5124
Bravo
AF:
0.260
Asia WGS
AF:
0.304
AC:
1057
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
0.66
DANN
Benign
0.58

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs11065450; hg19: chr12-121579657; API