ENST00000256644.8:c.157A>C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The ENST00000256644.8(LAMTOR5):āc.157A>Cā(p.Thr53Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000378 in 1,613,942 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/16 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
ENST00000256644.8 missense
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_006402.3 | c.157A>C | p.Thr53Pro | missense_variant | Exon 1 of 4 | NP_006393.2 | ||
LAMTOR5 | NM_001382293.1 | c.-90A>C | upstream_gene_variant | ENST00000602318.6 | NP_001369222.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000395 AC: 6AN: 152054Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251386Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135896
GnomAD4 exome AF: 0.0000376 AC: 55AN: 1461888Hom.: 0 Cov.: 32 AF XY: 0.0000344 AC XY: 25AN XY: 727244
GnomAD4 genome AF: 0.0000395 AC: 6AN: 152054Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74278
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.157A>C (p.T53P) alteration is located in exon 1 (coding exon 1) of the LAMTOR5 gene. This alteration results from a A to C substitution at nucleotide position 157, causing the threonine (T) at amino acid position 53 to be replaced by a proline (P). 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