7-98192803-T-C
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_014916.4(LMTK2):āc.2338T>Cā(p.Leu780=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000558 in 1,613,370 control chromosomes in the GnomAD database, with no homozygous occurrence. 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
Consequence
NM_014916.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LMTK2 | NM_014916.4 | c.2338T>C | p.Leu780= | synonymous_variant | 11/14 | ENST00000297293.6 | |
LMTK2 | XM_011515981.4 | c.2332T>C | p.Leu778= | synonymous_variant | 11/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LMTK2 | ENST00000297293.6 | c.2338T>C | p.Leu780= | synonymous_variant | 11/14 | 1 | NM_014916.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152006Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251224Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135790
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461364Hom.: 0 Cov.: 42 AF XY: 0.00000413 AC XY: 3AN XY: 726918
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152006Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74192
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at