rs200079151
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 2P and 17B. PM2BP4_StrongBP6_Very_StrongBP7BS1
The NM_024537.4(CARS2):c.1059C>T(p.Ile353=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000134 in 1,612,226 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. I353I) has been classified as Likely benign.
Frequency
Consequence
NM_024537.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CARS2 | NM_024537.4 | c.1059C>T | p.Ile353= | synonymous_variant | 11/15 | ENST00000257347.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CARS2 | ENST00000257347.9 | c.1059C>T | p.Ile353= | synonymous_variant | 11/15 | 1 | NM_024537.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000138 AC: 21AN: 152250Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000361 AC: 90AN: 249394Hom.: 0 AF XY: 0.000341 AC XY: 46AN XY: 135022
GnomAD4 exome AF: 0.000133 AC: 194AN: 1459858Hom.: 1 Cov.: 30 AF XY: 0.000142 AC XY: 103AN XY: 726062
GnomAD4 genome ? AF: 0.000144 AC: 22AN: 152368Hom.: 0 Cov.: 33 AF XY: 0.000174 AC XY: 13AN XY: 74510
ClinVar
Submissions by phenotype
Combined oxidative phosphorylation defect type 27 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Nov 12, 2023 | - - |
CARS2-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 18, 2019 | 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