rs747045010
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_016122.3(CEP83):c.479C>T(p.Ser160Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000793 in 1,513,538 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. S160S) has been classified as Likely benign.
Frequency
Consequence
NM_016122.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CEP83 | NM_016122.3 | c.479C>T | p.Ser160Leu | missense_variant | 6/17 | ENST00000397809.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CEP83 | ENST00000397809.10 | c.479C>T | p.Ser160Leu | missense_variant | 6/17 | 1 | NM_016122.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152046Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000971 AC: 2AN: 206024Hom.: 0 AF XY: 0.00000885 AC XY: 1AN XY: 113030
GnomAD4 exome AF: 0.00000661 AC: 9AN: 1361492Hom.: 0 Cov.: 24 AF XY: 0.00000889 AC XY: 6AN XY: 674890
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152046Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74266
ClinVar
Submissions by phenotype
Nephronophthisis 18 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Jul 06, 2022 | 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. 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: "Not Available"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Not Available"). ClinVar contains an entry for this variant (Variation ID: 578304). This variant has not been reported in the literature in individuals affected with CEP83-related conditions. This variant is present in population databases (rs747045010, gnomAD 0.002%). This sequence change replaces serine, which is neutral and polar, with leucine, which is neutral and non-polar, at codon 160 of the CEP83 protein (p.Ser160Leu). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at