10-100746267-A-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_000278.5(PAX2):āc.7A>Gā(p.Met3Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000192 in 1,613,252 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 Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 151916Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000804 AC: 2AN: 248710Hom.: 0 AF XY: 0.00000742 AC XY: 1AN XY: 134776
GnomAD4 exome AF: 0.0000205 AC: 30AN: 1461336Hom.: 0 Cov.: 35 AF XY: 0.0000124 AC XY: 9AN XY: 727014
GnomAD4 genome AF: 0.00000658 AC: 1AN: 151916Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74206
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 valine, which is neutral and non-polar, at codon 3 of the PAX2 protein (p.Met3Val). This variant is present in population databases (rs780113818, gnomAD 0.007%). This variant has not been reported in the literature in individuals affected with PAX2-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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