4-99885642-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_021970.4(LAMTOR3):c.137G>A(p.Arg46Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000026 in 1,613,090 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_021970.4 missense
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 |
---|---|---|---|---|---|---|---|---|
LAMTOR3 | NM_021970.4 | c.137G>A | p.Arg46Gln | missense_variant | Exon 5 of 7 | ENST00000499666.7 | NP_068805.1 | |
LAMTOR3 | NM_001243736.1 | c.116G>A | p.Arg39Gln | missense_variant | Exon 5 of 7 | NP_001230665.1 | ||
LAMTOR3 | NR_024170.1 | n.340G>A | non_coding_transcript_exon_variant | Exon 4 of 6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LAMTOR3 | ENST00000499666.7 | c.137G>A | p.Arg46Gln | missense_variant | Exon 5 of 7 | 1 | NM_021970.4 | ENSP00000424183.1 | ||
LAMTOR3 | ENST00000515100.1 | n.222G>A | non_coding_transcript_exon_variant | Exon 4 of 6 | 1 | |||||
LAMTOR3 | ENST00000226522.8 | c.116G>A | p.Arg39Gln | missense_variant | Exon 5 of 7 | 3 | ENSP00000226522.8 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152126Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 250490Hom.: 0 AF XY: 0.0000369 AC XY: 5AN XY: 135452
GnomAD4 exome AF: 0.0000240 AC: 35AN: 1460964Hom.: 0 Cov.: 30 AF XY: 0.0000206 AC XY: 15AN XY: 726826
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152126Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74298
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.137G>A (p.R46Q) alteration is located in exon 5 (coding exon 4) of the LAMTOR3 gene. This alteration results from a G to A substitution at nucleotide position 137, causing the arginine (R) at amino acid position 46 to be replaced by a glutamine (Q). 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