chr1-110403930-T-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001382293.1(LAMTOR5):c.204A>T(p.Glu68Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000372 in 1,613,990 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_001382293.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LAMTOR5 | NM_001382293.1 | c.204A>T | p.Glu68Asp | missense_variant | Exon 3 of 4 | ENST00000602318.6 | NP_001369222.1 | |
LAMTOR5 | NM_006402.3 | c.450A>T | p.Glu150Asp | missense_variant | Exon 3 of 4 | NP_006393.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152224Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251288Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135828
GnomAD4 exome AF: 0.0000369 AC: 54AN: 1461766Hom.: 0 Cov.: 30 AF XY: 0.0000358 AC XY: 26AN XY: 727200
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152224Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74378
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.450A>T (p.E150D) alteration is located in exon 3 (coding exon 3) of the LAMTOR5 gene. This alteration results from a A to T substitution at nucleotide position 450, causing the glutamic acid (E) at amino acid position 150 to be replaced by an aspartic acid (D). 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