NM_000278.5:c.932C>T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_000278.5(PAX2):c.932C>T(p.Ala311Val) variant causes a missense change. The variant allele was found at a frequency of 0.000222 in 1,607,932 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000278.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00115 AC: 175AN: 152086Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000414 AC: 104AN: 251442Hom.: 0 AF XY: 0.000287 AC XY: 39AN XY: 135902
GnomAD4 exome AF: 0.000125 AC: 182AN: 1455728Hom.: 1 Cov.: 31 AF XY: 0.000104 AC XY: 75AN XY: 724486
GnomAD4 genome AF: 0.00115 AC: 175AN: 152204Hom.: 0 Cov.: 31 AF XY: 0.00120 AC XY: 89AN XY: 74430
ClinVar
Submissions by phenotype
not provided Uncertain:1Other:1
Has been reported previously in an individual with retinal dystrophy (Carss et al., 2017); Has also been reported previously in an unaffected parent of a child anophthalmia but was not observed in the affected child (Gelb et al., 2001; Bower et al., 2012); In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; In addition, in silico splice predictors suggest this variant may lead to abnormal gene splicing; This variant is associated with the following publications: (PMID: 11180607, 22213154, 28041643) -
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Retinal dystrophy Pathogenic:1
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PAX2-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Renal coloboma syndrome;C4014925:Focal segmental glomerulosclerosis 7 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at