7-98151384-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_014916.4(LMTK2):c.379G>A(p.Gly127Arg) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.0000585 in 1,608,146 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014916.4 missense, splice_region
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 |
---|---|---|---|---|---|---|---|---|
LMTK2 | NM_014916.4 | c.379G>A | p.Gly127Arg | missense_variant, splice_region_variant | Exon 4 of 14 | ENST00000297293.6 | NP_055731.2 | |
LMTK2 | XM_011515981.4 | c.373G>A | p.Gly125Arg | missense_variant, splice_region_variant | Exon 4 of 14 | XP_011514283.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LMTK2 | ENST00000297293.6 | c.379G>A | p.Gly127Arg | missense_variant, splice_region_variant | Exon 4 of 14 | 1 | NM_014916.4 | ENSP00000297293.5 | ||
LMTK2 | ENST00000493372.1 | n.469G>A | splice_region_variant, non_coding_transcript_exon_variant | Exon 4 of 4 | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000658 AC: 10AN: 152058Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000135 AC: 34AN: 251114Hom.: 0 AF XY: 0.0000810 AC XY: 11AN XY: 135736
GnomAD4 exome AF: 0.0000577 AC: 84AN: 1455970Hom.: 0 Cov.: 29 AF XY: 0.0000635 AC XY: 46AN XY: 724756
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152176Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74398
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.379G>A (p.G127R) alteration is located in exon 4 (coding exon 4) of the LMTK2 gene. This alteration results from a G to A substitution at nucleotide position 379, causing the glycine (G) at amino acid position 127 to be replaced by an arginine (R). 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