chr16-75631248-G-A
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBS1BS2
The NM_005548.3(KARS1):c.1258C>T(p.Arg420Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00292 in 1,613,744 control chromosomes in the GnomAD database, including 12 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_005548.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KARS1 | NM_005548.3 | c.1258C>T | p.Arg420Cys | missense_variant | Exon 10 of 14 | ENST00000302445.8 | NP_005539.1 | |
KARS1 | NM_001130089.2 | c.1342C>T | p.Arg448Cys | missense_variant | Exon 11 of 15 | NP_001123561.1 | ||
KARS1 | NM_001378148.1 | c.790C>T | p.Arg264Cys | missense_variant | Exon 10 of 14 | NP_001365077.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00193 AC: 294AN: 152164Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.00149 AC: 374AN: 250636Hom.: 2 AF XY: 0.00154 AC XY: 209AN XY: 135536
GnomAD4 exome AF: 0.00302 AC: 4413AN: 1461462Hom.: 11 Cov.: 32 AF XY: 0.00290 AC XY: 2111AN XY: 727044
GnomAD4 genome AF: 0.00193 AC: 294AN: 152282Hom.: 1 Cov.: 33 AF XY: 0.00161 AC XY: 120AN XY: 74456
ClinVar
Submissions by phenotype
not provided Benign:4
KARS1: BS1, BS2 -
This variant is associated with the following publications: (PMID: 26762739) -
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not specified Benign:2
Arg448Cys in exon 11 of KARS: This variant is not expected to have clinical sign ificance because it has been identified in 0.3% (26/8600) of European American c hromosomes from a broad population by the NHLBI Exome Sequencing Project (http:/ /evs.gs.washington.edu/EVS; dbSNP rs77573084). -
Variant summary: KARS1 c.1342C>T (p.Arg448Cys) results in a non-conservative amino acid change located in the tRNA synthetases class II (D, K and N) domain (IPR004364) of the encoded protein sequence. Three of four in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.0029 in 1613744 control chromosomes in the gnomAD database, including 12 homozygotes. The observed variant frequency is approximately 2.61 fold of the estimated maximal expected allele frequency for a pathogenic variant in KARS1 causing Leukoencephalopathy, progressive, infantile-onset, with or without deafness phenotype (0.0011). c.1342C>T has been reported in the presumed heterozygous state in the literature in association with hereditary motor neuropathy (example, Antoniadi_2015) without strong evidence for causality. These report(s) do not provide unequivocal conclusions about association of the variant with KARS1-related conditions. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. ClinVar contains an entry for this variant (Variation ID: 226679). Based on the evidence outlined above, the variant was classified as likely benign. -
KARS1-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at