9-6533027-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_000170.3(GLDC):c.3053C>T(p.Ala1018Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000988 in 1,609,610 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_000170.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152172Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000756 AC: 19AN: 251426Hom.: 0 AF XY: 0.0000883 AC XY: 12AN XY: 135880
GnomAD4 exome AF: 0.000104 AC: 151AN: 1457320Hom.: 1 Cov.: 29 AF XY: 0.0000965 AC XY: 70AN XY: 725308
GnomAD4 genome AF: 0.0000525 AC: 8AN: 152290Hom.: 0 Cov.: 31 AF XY: 0.0000403 AC XY: 3AN XY: 74464
ClinVar
Submissions by phenotype
Glycine encephalopathy Uncertain:1
This sequence change replaces alanine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 1018 of the GLDC protein (p.Ala1018Val). This variant is present in population databases (rs150149798, gnomAD 0.04%). This variant has not been reported in the literature in individuals affected with GLDC-related conditions. 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: "Possibly Damaging"; 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