rs369646534
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001382293.1(LAMTOR5):c.-44G>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000186 in 1,614,104 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001382293.1 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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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.-44G>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 4 | ENST00000602318.6 | NP_001369222.1 | ||
LAMTOR5 | NM_001382293.1 | c.-44G>T | 5_prime_UTR_variant | Exon 1 of 4 | ENST00000602318.6 | NP_001369222.1 | ||
LAMTOR5 | NM_006402.3 | c.203G>T | p.Arg68Leu | missense_variant | Exon 1 of 4 | NP_006393.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LAMTOR5 | ENST00000602318.6 | c.-44G>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 4 | 1 | NM_001382293.1 | ENSP00000473439.1 | |||
LAMTOR5 | ENST00000602318.6 | c.-44G>T | 5_prime_UTR_variant | Exon 1 of 4 | 1 | NM_001382293.1 | ENSP00000473439.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152226Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251036Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135760
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461878Hom.: 0 Cov.: 32 AF XY: 0.00000275 AC XY: 2AN XY: 727240
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152226Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74374
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at