rs11765552
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_014916.4(LMTK2):c.2338T>A(p.Leu780Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.477 in 1,613,060 control chromosomes in the GnomAD database, including 199,132 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_014916.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LMTK2 | NM_014916.4 | c.2338T>A | p.Leu780Met | missense_variant | 11/14 | ENST00000297293.6 | |
LMTK2 | XM_011515981.4 | c.2332T>A | p.Leu778Met | missense_variant | 11/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LMTK2 | ENST00000297293.6 | c.2338T>A | p.Leu780Met | missense_variant | 11/14 | 1 | NM_014916.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.374 AC: 56768AN: 151962Hom.: 13464 Cov.: 32
GnomAD3 exomes AF: 0.402 AC: 100889AN: 251224Hom.: 24268 AF XY: 0.411 AC XY: 55797AN XY: 135790
GnomAD4 exome AF: 0.488 AC: 712340AN: 1460980Hom.: 185669 Cov.: 42 AF XY: 0.483 AC XY: 351072AN XY: 726748
GnomAD4 genome ? AF: 0.373 AC: 56752AN: 152080Hom.: 13463 Cov.: 32 AF XY: 0.364 AC XY: 27051AN XY: 74292
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at