rs753458157
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_153240.5(NPHP3):c.187G>C(p.Gly63Arg) variant causes a missense change. The variant allele was found at a frequency of 0.00000704 in 1,563,476 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G63E) has been classified as Uncertain significance.
Frequency
Consequence
NM_153240.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NPHP3 | NM_153240.5 | c.187G>C | p.Gly63Arg | missense_variant | 1/27 | ENST00000337331.10 | |
NPHP3-AS1 | NR_002811.2 | n.420C>G | non_coding_transcript_exon_variant | 1/11 | |||
NPHP3-ACAD11 | NR_037804.1 | n.291G>C | non_coding_transcript_exon_variant | 1/45 | |||
NPHP3-AS1 | NR_152743.1 | n.420C>G | non_coding_transcript_exon_variant | 1/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NPHP3 | ENST00000337331.10 | c.187G>C | p.Gly63Arg | missense_variant | 1/27 | 1 | NM_153240.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152152Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000566 AC: 1AN: 176792Hom.: 0 AF XY: 0.0000100 AC XY: 1AN XY: 99556
GnomAD4 exome AF: 0.00000709 AC: 10AN: 1411324Hom.: 0 Cov.: 31 AF XY: 0.00000999 AC XY: 7AN XY: 700702
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152152Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74338
ClinVar
Submissions by phenotype
Nephronophthisis Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Aug 23, 2022 | 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: 531620). 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: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). 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. This variant is present in population databases (rs753458157, gnomAD 0.001%). This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 63 of the NPHP3 protein (p.Gly63Arg). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at