1-110406321-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_001382293.1(LAMTOR5):c.94G>T(p.Gly32Cys) variant causes a missense change. The variant allele was found at a frequency of 0.00000312 in 1,600,694 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G32S) has been classified as Uncertain significance.
Frequency
Consequence
NM_001382293.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LAMTOR5 | NM_001382293.1 | c.94G>T | p.Gly32Cys | missense_variant | Exon 2 of 4 | ENST00000602318.6 | NP_001369222.1 | |
LAMTOR5 | NM_006402.3 | c.340G>T | p.Gly114Cys | missense_variant | Exon 2 of 4 | NP_006393.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152088Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000820 AC: 2AN: 243944Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 132004
GnomAD4 exome AF: 0.00000276 AC: 4AN: 1448606Hom.: 0 Cov.: 27 AF XY: 0.00000139 AC XY: 1AN XY: 720884
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152088Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74290
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at