X-121047722-G-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_ModerateBP6BS2_Supporting
The NM_012084.4(GLUD2):c.38G>T(p.Arg13Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000105 in 1,101,602 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 41 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_012084.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GLUD2 | NM_012084.4 | c.38G>T | p.Arg13Leu | missense_variant | 1/1 | ENST00000328078.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GLUD2 | ENST00000328078.3 | c.38G>T | p.Arg13Leu | missense_variant | 1/1 | NM_012084.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000447 AC: 5AN: 111798Hom.: 0 Cov.: 22 AF XY: 0.0000584 AC XY: 2AN XY: 34230
GnomAD3 exomes AF: 0.0000889 AC: 10AN: 112495Hom.: 0 AF XY: 0.0000527 AC XY: 2AN XY: 37971
GnomAD4 exome AF: 0.000112 AC: 111AN: 989804Hom.: 0 Cov.: 29 AF XY: 0.000124 AC XY: 39AN XY: 315368
GnomAD4 genome AF: 0.0000447 AC: 5AN: 111798Hom.: 0 Cov.: 22 AF XY: 0.0000584 AC XY: 2AN XY: 34230
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 28, 2023 | The c.38G>T (p.R13L) alteration is located in exon 1 (coding exon 1) of the GLUD2 gene. This alteration results from a G to T substitution at nucleotide position 38, causing the arginine (R) at amino acid position 13 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2023 | GLUD2: BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at