chr16-75628590-G-A
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_005548.3(KARS1):c.1674C>T(p.Leu558Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000915 in 1,614,046 control chromosomes in the GnomAD database, including 5 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 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
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KARS1 | NM_005548.3 | c.1674C>T | p.Leu558Leu | synonymous_variant | Exon 13 of 14 | ENST00000302445.8 | NP_005539.1 | |
KARS1 | NM_001130089.2 | c.1758C>T | p.Leu586Leu | synonymous_variant | Exon 14 of 15 | NP_001123561.1 | ||
KARS1 | NM_001378148.1 | c.1206C>T | p.Leu402Leu | synonymous_variant | Exon 13 of 14 | NP_001365077.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00240 AC: 365AN: 152240Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00134 AC: 337AN: 251416Hom.: 2 AF XY: 0.00118 AC XY: 160AN XY: 135896
GnomAD4 exome AF: 0.000761 AC: 1113AN: 1461688Hom.: 5 Cov.: 32 AF XY: 0.000730 AC XY: 531AN XY: 727148
GnomAD4 genome AF: 0.00239 AC: 364AN: 152358Hom.: 0 Cov.: 33 AF XY: 0.00225 AC XY: 168AN XY: 74510
ClinVar
Submissions by phenotype
not provided Benign:7
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KARS1: BP4, BP7 -
not specified Benign:3
Leu586Leu in exon 14 of KARS: This variant is not expected to have clinical sign ificance because it does not alter an amino acid residue and is not located with in the splice consensus sequence. It has been identified in 0.6% (27/4396) of Af rican American chromosomes from a broad population by the NHLBI Exome Sequencing Project (http://evs.gs.washington.edu/EVS; dbSNP rs143267922). -
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at