13-110642407-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_024537.4(CARS2):c.1531G>A(p.Ala511Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00112 in 1,585,428 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_024537.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CARS2 | NM_024537.4 | c.1531G>A | p.Ala511Thr | missense_variant | 14/15 | ENST00000257347.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CARS2 | ENST00000257347.9 | c.1531G>A | p.Ala511Thr | missense_variant | 14/15 | 1 | NM_024537.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00157 AC: 239AN: 152242Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.00147 AC: 300AN: 203930Hom.: 1 AF XY: 0.00137 AC XY: 151AN XY: 110192
GnomAD4 exome AF: 0.00107 AC: 1539AN: 1433068Hom.: 6 Cov.: 33 AF XY: 0.00105 AC XY: 744AN XY: 710536
GnomAD4 genome AF: 0.00157 AC: 239AN: 152360Hom.: 1 Cov.: 33 AF XY: 0.00208 AC XY: 155AN XY: 74514
ClinVar
Submissions by phenotype
Combined oxidative phosphorylation defect type 27 Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Jan 17, 2022 | - - |
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jun 01, 2024 | CARS2: BP4, BS2 - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 02, 2020 | - - |
CARS2-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 09, 2020 | 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