rs3751142
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_002562.6(P2RX7):c.1602G>T(p.Leu534=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0969 in 1,611,842 control chromosomes in the GnomAD database, including 10,317 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 0.12 ( 1446 hom., cov: 33)
Exomes 𝑓: 0.094 ( 8871 hom. )
Consequence
P2RX7
NM_002562.6 synonymous
NM_002562.6 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.00
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.62).
BP7
?
Synonymous conserved (PhyloP=3 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
P2RX7 | NM_002562.6 | c.1602G>T | p.Leu534= | synonymous_variant | 13/13 | ENST00000328963.10 | |
LOC105370032 | XR_001749352.3 | n.327+18882C>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
P2RX7 | ENST00000328963.10 | c.1602G>T | p.Leu534= | synonymous_variant | 13/13 | 1 | NM_002562.6 | P1 | |
ENST00000652651.1 | n.3548+1585C>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.123 AC: 18641AN: 152170Hom.: 1434 Cov.: 33
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GnomAD3 exomes AF: 0.142 AC: 34790AN: 244858Hom.: 3771 AF XY: 0.133 AC XY: 17612AN XY: 132822
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GnomAD4 exome AF: 0.0943 AC: 137569AN: 1459554Hom.: 8871 Cov.: 41 AF XY: 0.0940 AC XY: 68221AN XY: 726014
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GnomAD4 genome ? AF: 0.123 AC: 18685AN: 152288Hom.: 1446 Cov.: 33 AF XY: 0.127 AC XY: 9428AN XY: 74462
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at