7-98187015-C-T
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_014916.4(LMTK2):c.998+17C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.476 in 1,596,282 control chromosomes in the GnomAD database, including 196,711 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.37 ( 13406 hom., cov: 33)
Exomes 𝑓: 0.49 ( 183305 hom. )
Consequence
LMTK2
NM_014916.4 intron
NM_014916.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.617
Genes affected
LMTK2 (HGNC:17880): (lemur tyrosine kinase 2) The protein encoded by this gene belongs to the protein kinase superfamily and the protein tyrosine kinase family. It contains N-terminal transmembrane helices and a long C-terminal cytoplasmic tail with serine/threonine/tyrosine kinase activity. This protein interacts with several other proteins, such as Inhibitor-2 (Inh2), protein phosphatase-1 (PP1C), p35, and myosin VI. It phosporylates other proteins, and is itself also phosporylated when interacting with cyclin-dependent kinase 5 (cdk5)/p35 complex. This protein involves in nerve growth factor (NGF)-TrkA signalling, and also plays a critical role in endosomal membrane trafficking. Mouse studies suggested an essential role of this protein in spermatogenesis. [provided by RefSeq, Oct 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.532 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LMTK2 | NM_014916.4 | c.998+17C>T | intron_variant | ENST00000297293.6 | |||
LMTK2 | XM_011515981.4 | c.992+17C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LMTK2 | ENST00000297293.6 | c.998+17C>T | intron_variant | 1 | NM_014916.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.373 AC: 56662AN: 152012Hom.: 13407 Cov.: 33
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GnomAD3 exomes AF: 0.405 AC: 96530AN: 238114Hom.: 23378 AF XY: 0.415 AC XY: 53363AN XY: 128538
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GnomAD4 exome AF: 0.487 AC: 703442AN: 1444152Hom.: 183305 Cov.: 29 AF XY: 0.483 AC XY: 346528AN XY: 717764
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GnomAD4 genome ? AF: 0.372 AC: 56645AN: 152130Hom.: 13406 Cov.: 33 AF XY: 0.363 AC XY: 27013AN XY: 74360
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at