7-98154806-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_014916.4(LMTK2):c.499G>A(p.Val167Met) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000229 in 1,613,916 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014916.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152198Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000676 AC: 17AN: 251362Hom.: 0 AF XY: 0.0000736 AC XY: 10AN XY: 135842
GnomAD4 exome AF: 0.0000192 AC: 28AN: 1461600Hom.: 0 Cov.: 30 AF XY: 0.0000165 AC XY: 12AN XY: 727116
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152316Hom.: 0 Cov.: 33 AF XY: 0.0000940 AC XY: 7AN XY: 74486
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.499G>A (p.V167M) alteration is located in exon 5 (coding exon 5) of the LMTK2 gene. This alteration results from a G to A substitution at nucleotide position 499, causing the valine (V) at amino acid position 167 to be replaced by a methionine (M). 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