11-58709944-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_201648.3(GLYAT):c.713G>A(p.Arg238Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000576 in 1,613,922 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R238W) has been classified as Uncertain significance.
Frequency
Consequence
NM_201648.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GLYAT | NM_201648.3 | c.713G>A | p.Arg238Gln | missense_variant | Exon 6 of 6 | ENST00000344743.8 | NP_964011.2 | |
GLYAT | XM_017017087.1 | c.521G>A | p.Arg174Gln | missense_variant | Exon 6 of 6 | XP_016872576.1 | ||
GLYAT | NM_005838.4 | c.*642G>A | downstream_gene_variant | NP_005829.3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152230Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000837 AC: 21AN: 250912Hom.: 0 AF XY: 0.0000737 AC XY: 10AN XY: 135622
GnomAD4 exome AF: 0.0000575 AC: 84AN: 1461692Hom.: 0 Cov.: 32 AF XY: 0.0000674 AC XY: 49AN XY: 727146
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152230Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74386
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.713G>A (p.R238Q) alteration is located in exon 6 (coding exon 5) of the GLYAT gene. This alteration results from a G to A substitution at nucleotide position 713, causing the arginine (R) at amino acid position 238 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at