17-3688098-T-C
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_002561.4(P2RX5):āc.895A>Gā(p.Arg299Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000252 in 1,588,122 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.000013 ( 0 hom., cov: 29)
Exomes š: 0.0000014 ( 0 hom. )
Consequence
P2RX5
NM_002561.4 missense
NM_002561.4 missense
Scores
6
8
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.03
Genes affected
P2RX5 (HGNC:8536): (purinergic receptor P2X 5) The product of this gene belongs to the family of purinoceptors for ATP. This receptor functions as a ligand-gated ion channel. Alternative splicing results in multiple transcript variants. Read-through transcription also exists between this gene and the neighboring downstream gene, TAX1BP3 (Tax1 binding protein 3). [provided by RefSeq, Mar 2011]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
P2RX5 | NM_002561.4 | c.895A>G | p.Arg299Gly | missense_variant | 9/12 | ENST00000225328.10 | |
P2RX5-TAX1BP3 | NR_037928.1 | n.1294A>G | non_coding_transcript_exon_variant | 9/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
P2RX5 | ENST00000225328.10 | c.895A>G | p.Arg299Gly | missense_variant | 9/12 | 1 | NM_002561.4 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151176Hom.: 0 Cov.: 29
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GnomAD3 exomes AF: 0.00000428 AC: 1AN: 233620Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 126324
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GnomAD4 exome AF: 0.00000139 AC: 2AN: 1436946Hom.: 0 Cov.: 28 AF XY: 0.00000140 AC XY: 1AN XY: 714824
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GnomAD4 genome AF: 0.0000132 AC: 2AN: 151176Hom.: 0 Cov.: 29 AF XY: 0.0000136 AC XY: 1AN XY: 73784
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
Eigen
Uncertain
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T;T;T;T;T
M_CAP
Benign
T
MetaRNN
Uncertain
T;T;T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
N;N;N;N;N;N;N
PrimateAI
Benign
T
Sift4G
Uncertain
D;D;D;D;D;D
Polyphen
0.76, 0.45, 0.69, 0.73
.;P;P;P;.;P
Vest4
MVP
MPC
0.18
ClinPred
D
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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