chr1-110404034-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001382293.1(LAMTOR5):c.100C>T(p.Arg34Cys) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.0000973 in 1,613,462 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001382293.1 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LAMTOR5 | NM_001382293.1 | c.100C>T | p.Arg34Cys | missense_variant, splice_region_variant | Exon 3 of 4 | ENST00000602318.6 | NP_001369222.1 | |
LAMTOR5 | NM_006402.3 | c.346C>T | p.Arg116Cys | missense_variant, splice_region_variant | Exon 3 of 4 | NP_006393.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152086Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000399 AC: 10AN: 250492Hom.: 0 AF XY: 0.0000369 AC XY: 5AN XY: 135406
GnomAD4 exome AF: 0.0000992 AC: 145AN: 1461376Hom.: 0 Cov.: 30 AF XY: 0.000106 AC XY: 77AN XY: 726986
GnomAD4 genome AF: 0.0000789 AC: 12AN: 152086Hom.: 0 Cov.: 32 AF XY: 0.0000808 AC XY: 6AN XY: 74278
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.346C>T (p.R116C) alteration is located in exon 3 (coding exon 3) of the LAMTOR5 gene. This alteration results from a C to T substitution at nucleotide position 346, causing the arginine (R) at amino acid position 116 to be replaced by a cysteine (C). 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