NM_003055.3:c.88C>T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_003055.3(SLC18A3):c.88C>T(p.Arg30Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000208 in 1,607,882 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_003055.3 missense
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: 0.000131 AC: 20AN: 152250Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.000191 AC: 45AN: 236136Hom.: 0 AF XY: 0.000195 AC XY: 25AN XY: 128528
GnomAD4 exome AF: 0.000216 AC: 315AN: 1455514Hom.: 0 Cov.: 80 AF XY: 0.000236 AC XY: 171AN XY: 723618
GnomAD4 genome AF: 0.000131 AC: 20AN: 152368Hom.: 0 Cov.: 34 AF XY: 0.0000939 AC XY: 7AN XY: 74514
ClinVar
Submissions by phenotype
Congenital myasthenic syndrome 21 Uncertain:1
This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868]. -
not provided Uncertain:1
This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 30 of the SLC18A3 protein (p.Arg30Trp). This variant is present in population databases (rs8187735, gnomAD 0.04%). This variant has not been reported in the literature in individuals affected with SLC18A3-related conditions. ClinVar contains an entry for this variant (Variation ID: 1032111). 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. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at