12-132618913-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_170682.4(P2RX2):c.97G>A(p.Val33Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000035 in 1,344,184 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_170682.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000668 AC: 1AN: 149730Hom.: 0 Cov.: 29
GnomAD3 exomes AF: 0.00000854 AC: 1AN: 117088Hom.: 0 AF XY: 0.0000154 AC XY: 1AN XY: 64934
GnomAD4 exome AF: 0.0000385 AC: 46AN: 1194454Hom.: 0 Cov.: 31 AF XY: 0.0000344 AC XY: 20AN XY: 582234
GnomAD4 genome AF: 0.00000668 AC: 1AN: 149730Hom.: 0 Cov.: 29 AF XY: 0.0000137 AC XY: 1AN XY: 73050
ClinVar
Submissions by phenotype
not provided Uncertain:1
Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). This sequence change replaces valine, which is neutral and non-polar, with methionine, which is neutral and non-polar, at codon 33 of the P2RX2 protein (p.Val33Met). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with P2RX2-related conditions. ClinVar contains an entry for this variant (Variation ID: 1490285). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at