chr16-75627987-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2PP3_ModeratePP5
The NM_005548.3(KARS1):c.1702C>T(p.Leu568Phe) variant causes a missense change. The variant allele was found at a frequency of 0.00000698 in 1,433,442 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Synonymous variant affecting the same amino acid position (i.e. L568L) has been classified as Likely benign.
Frequency
Consequence
NM_005548.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KARS1 | NM_005548.3 | c.1702C>T | p.Leu568Phe | missense_variant | 14/14 | ENST00000302445.8 | |
KARS1 | NM_001130089.2 | c.1786C>T | p.Leu596Phe | missense_variant | 15/15 | ||
KARS1 | NM_001378148.1 | c.1234C>T | p.Leu412Phe | missense_variant | 14/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KARS1 | ENST00000302445.8 | c.1702C>T | p.Leu568Phe | missense_variant | 14/14 | 1 | NM_005548.3 | A1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000798 AC: 2AN: 250648Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135614
GnomAD4 exome AF: 0.00000698 AC: 10AN: 1433442Hom.: 0 Cov.: 25 AF XY: 0.00000699 AC XY: 5AN XY: 715020
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
LEUKOENCEPHALOPATHY, PROGRESSIVE, INFANTILE-ONSET, WITH DEAFNESS Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Mar 01, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at