rs77111027
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_002562.6(P2RX7):c.1745C>T(p.Pro582Leu) variant causes a missense change. The variant allele was found at a frequency of 0.000354 in 1,553,440 control chromosomes in the GnomAD database, including 2 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 0.0019 ( 2 hom., cov: 33)
Exomes 𝑓: 0.00019 ( 0 hom. )
Consequence
P2RX7
NM_002562.6 missense
NM_002562.6 missense
Scores
2
8
7
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 5.62
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 -8 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.0063925385).
BS2
High Homozygotes in GnomAd4 at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
P2RX7 | NM_002562.6 | c.1745C>T | p.Pro582Leu | missense_variant | 13/13 | ENST00000328963.10 | |
LOC105370032 | XR_001749352.3 | n.327+18739G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
P2RX7 | ENST00000328963.10 | c.1745C>T | p.Pro582Leu | missense_variant | 13/13 | 1 | NM_002562.6 | P1 | |
ENST00000652651.1 | n.3548+1442G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.00185 AC: 282AN: 152132Hom.: 2 Cov.: 33
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GnomAD3 exomes AF: 0.000392 AC: 62AN: 158146Hom.: 0 AF XY: 0.000250 AC XY: 21AN XY: 84068
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GnomAD4 exome AF: 0.000190 AC: 266AN: 1401190Hom.: 0 Cov.: 36 AF XY: 0.000166 AC XY: 115AN XY: 691410
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GnomAD4 genome AF: 0.00187 AC: 284AN: 152250Hom.: 2 Cov.: 33 AF XY: 0.00161 AC XY: 120AN XY: 74434
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Uncertain
T
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Uncertain
T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
D
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M
MutationTaster
Benign
D;D;D;D
PrimateAI
Uncertain
T
REVEL
Benign
Sift4G
Pathogenic
D
Polyphen
D
Vest4
MVP
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at