NM_001382293.1:c.238G>A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001382293.1(LAMTOR5):c.238G>A(p.Asp80Asn) variant causes a missense change. The variant allele was found at a frequency of 0.0000249 in 1,606,764 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
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LAMTOR5 | NM_001382293.1 | c.238G>A | p.Asp80Asn | missense_variant | Exon 4 of 4 | ENST00000602318.6 | NP_001369222.1 | |
LAMTOR5 | NM_006402.3 | c.484G>A | p.Asp162Asn | missense_variant | Exon 4 of 4 | NP_006393.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152102Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000518 AC: 13AN: 251168Hom.: 0 AF XY: 0.0000810 AC XY: 11AN XY: 135802
GnomAD4 exome AF: 0.0000234 AC: 34AN: 1454662Hom.: 0 Cov.: 30 AF XY: 0.0000319 AC XY: 23AN XY: 722032
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152102Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74298
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.484G>A (p.D162N) alteration is located in exon 4 (coding exon 4) of the LAMTOR5 gene. This alteration results from a G to A substitution at nucleotide position 484, causing the aspartic acid (D) at amino acid position 162 to be replaced by an asparagine (N). 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