rs112749193
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_153240.5(NPHP3):c.3570+9G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0003 in 1,613,722 control chromosomes in the GnomAD database, including 4 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_153240.5 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NPHP3 | ENST00000337331.10 | c.3570+9G>T | intron_variant | Intron 24 of 26 | 1 | NM_153240.5 | ENSP00000338766.5 | |||
NPHP3-ACAD11 | ENST00000632629.1 | c.216+9G>T | intron_variant | Intron 1 of 4 | 2 | ENSP00000488520.1 |
Frequencies
GnomAD3 genomes AF: 0.00118 AC: 180AN: 152156Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000320 AC: 80AN: 250226Hom.: 0 AF XY: 0.000236 AC XY: 32AN XY: 135418
GnomAD4 exome AF: 0.000207 AC: 302AN: 1461448Hom.: 3 Cov.: 31 AF XY: 0.000194 AC XY: 141AN XY: 727034
GnomAD4 genome AF: 0.00120 AC: 182AN: 152274Hom.: 1 Cov.: 32 AF XY: 0.00110 AC XY: 82AN XY: 74450
ClinVar
Submissions by phenotype
not specified Benign:3
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This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Kidney disorder Uncertain:1
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Nephronophthisis 3;C2673885:NPHP3-related Meckel-like syndrome;C3715199:Renal-hepatic-pancreatic dysplasia 1 Benign:1
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Nephronophthisis Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at