chr15-41505472-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.
The NM_002344.6(LTK):c.1756C>G(p.Arg586Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000235 in 1,614,102 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R586H) has been classified as Uncertain significance.
Frequency
Consequence
NM_002344.6 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LTK | NM_002344.6 | c.1756C>G | p.Arg586Gly | missense_variant | 14/20 | ENST00000263800.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LTK | ENST00000263800.11 | c.1756C>G | p.Arg586Gly | missense_variant | 14/20 | 1 | NM_002344.6 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152176Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250814Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135668
GnomAD4 exome AF: 0.0000239 AC: 35AN: 1461808Hom.: 0 Cov.: 33 AF XY: 0.0000303 AC XY: 22AN XY: 727202
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152294Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74458
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 10, 2022 | The c.1756C>G (p.R586G) alteration is located in exon 14 (coding exon 14) of the LTK gene. This alteration results from a C to G substitution at nucleotide position 1756, causing the arginine (R) at amino acid position 586 to be replaced by a glycine (G). 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