rs758002007
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_005619.5(RTN2):c.257C>T(p.Pro86Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000103 in 1,451,198 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 Uncertain significance (★).
Frequency
Consequence
NM_005619.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000418 AC: 1AN: 238992Hom.: 0 AF XY: 0.00000765 AC XY: 1AN XY: 130760
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1451198Hom.: 0 Cov.: 32 AF XY: 0.00000969 AC XY: 7AN XY: 722314
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Spastic paraplegia Uncertain:1
This sequence change replaces proline with leucine at codon 86 of the RTN2 protein (p.Pro86Leu). The proline residue is weakly conserved and there is a moderate physicochemical difference between proline and leucine. This variant is present in population databases at a very low frequency (rs758002007, ExAC <0.01%) but has not been reported in the literature in individuals with a RTN2-related disease. Algorithms developed to predict the effect of missense changes on protein structure and function do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). In summary, this variant is a rare missense change with uncertain impact on protein function. There is no indication that it causes disease, but the available evidence is currently insufficient to prove that conclusively. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at