1-156054919-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_014017.4(LAMTOR2):c.30G>A(p.Val10Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,612,842 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_014017.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LAMTOR2 | ENST00000368305.9 | c.30G>A | p.Val10Val | synonymous_variant | Exon 1 of 4 | 1 | NM_014017.4 | ENSP00000357288.4 | ||
LAMTOR2 | ENST00000368302.3 | c.30G>A | p.Val10Val | synonymous_variant | Exon 1 of 4 | 3 | ENSP00000357285.3 | |||
LAMTOR2 | ENST00000368304.9 | c.30G>A | p.Val10Val | synonymous_variant | Exon 1 of 3 | 2 | ENSP00000357287.5 | |||
LAMTOR2 | ENST00000489664.1 | n.99G>A | non_coding_transcript_exon_variant | Exon 1 of 2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152224Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000402 AC: 1AN: 249060Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135186
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1460618Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 726588
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152224Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74374
ClinVar
Submissions by phenotype
not provided Uncertain:1
This sequence change affects codon 10 of the LAMTOR2 mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the LAMTOR2 protein. This variant is present in population databases (no rsID available, gnomAD 0.003%). This variant has not been reported in the literature in individuals affected with LAMTOR2-related conditions. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. 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