chr3-132719848-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP6
The NM_153240.5(NPHP3):c.394-18C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000389 in 1,540,578 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_153240.5 intron
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 AF: 0.0000265 AC: 4AN: 151024Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000425 AC: 1AN: 235072Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 127410
GnomAD4 exome AF: 0.00000144 AC: 2AN: 1389554Hom.: 0 Cov.: 24 AF XY: 0.00000145 AC XY: 1AN XY: 690940
GnomAD4 genome AF: 0.0000265 AC: 4AN: 151024Hom.: 0 Cov.: 32 AF XY: 0.0000271 AC XY: 2AN XY: 73722
ClinVar
Submissions by phenotype
Nephronophthisis Uncertain:1
This sequence change falls in intron 1 of the NPHP3 gene. It does not directly change the encoded amino acid sequence of the NPHP3 protein. This variant is present in population databases (no rsID available, gnomAD 0.009%). This variant has not been reported in the literature in individuals affected with NPHP3-related conditions. ClinVar contains an entry for this variant (Variation ID: 262712). 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. -
not specified Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at