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 (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R420H) has been classified as Uncertain significance.
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KARS1 | NM_005548.3 | c.1258C>T | p.Arg420Cys | missense_variant | 10/14 | ENST00000302445.8 | |
KARS1 | NM_001130089.2 | c.1342C>T | p.Arg448Cys | missense_variant | 11/15 | ||
KARS1 | NM_001378148.1 | c.790C>T | p.Arg264Cys | missense_variant | 10/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KARS1 | ENST00000302445.8 | c.1258C>T | p.Arg420Cys | missense_variant | 10/14 | 1 | NM_005548.3 | A1 | |
KARS1 | ENST00000319410.9 | c.1342C>T | p.Arg448Cys | missense_variant | 11/15 | 1 | P4 | ||
KARS1 | ENST00000568378.5 | c.147-3259C>T | intron_variant | 5 | |||||
KARS1 | ENST00000564578.5 | c.*801C>T | 3_prime_UTR_variant, NMD_transcript_variant | 10/14 | 5 |
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
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Aug 01, 2023 | KARS1: BS2 - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 09, 2020 | This variant is associated with the following publications: (PMID: 26762739) - |
Likely benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Oct 14, 2023 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2024 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Nov 24, 2014 | 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). - |
KARS1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 11, 2022 | 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