chr11-57348212-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_002559.5(P2RX3):c.434G>A(p.Arg145Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00105 in 1,602,536 control chromosomes in the GnomAD database, including 13 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R145W) has been classified as Uncertain significance.
Frequency
Consequence
NM_002559.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
P2RX3 | NM_002559.5 | c.434G>A | p.Arg145Gln | missense_variant | 5/12 | ENST00000263314.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
P2RX3 | ENST00000263314.3 | c.434G>A | p.Arg145Gln | missense_variant | 5/12 | 1 | NM_002559.5 | P1 | |
P2RX3 | ENST00000534820.1 | c.98G>A | p.Arg33Gln | missense_variant, NMD_transcript_variant | 2/5 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00490 AC: 745AN: 152190Hom.: 4 Cov.: 32
GnomAD3 exomes AF: 0.00152 AC: 349AN: 229886Hom.: 4 AF XY: 0.00110 AC XY: 136AN XY: 123688
GnomAD4 exome AF: 0.000650 AC: 943AN: 1450228Hom.: 9 Cov.: 31 AF XY: 0.000564 AC XY: 406AN XY: 719990
GnomAD4 genome AF: 0.00488 AC: 744AN: 152308Hom.: 4 Cov.: 32 AF XY: 0.00441 AC XY: 328AN XY: 74456
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | May 21, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at