10-100746268-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_000278.5(PAX2):āc.8T>Cā(p.Met3Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,461,366 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_000278.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.0000161 AC: 4AN: 248708Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 134772
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461366Hom.: 0 Cov.: 35 AF XY: 0.00000275 AC XY: 2AN XY: 727018
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Renal coloboma syndrome;C4014925:Focal segmental glomerulosclerosis 7 Uncertain:1
This sequence change replaces methionine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 3 of the PAX2 protein (p.Met3Thr). This variant is present in population databases (rs754968736, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with PAX2-related conditions. 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: "Not Available"; PolyPhen-2: "Benign"; Align-GVGD: "Not Available"). 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