13-110683120-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.586G>A(p.Asp196Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00176 in 1,595,142 control chromosomes in the GnomAD database, including 53 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D196H) has been classified as Uncertain significance.
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.586G>A | p.Asp196Asn | missense_variant | 6/15 | ENST00000257347.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CARS2 | ENST00000257347.9 | c.586G>A | p.Asp196Asn | missense_variant | 6/15 | 1 | NM_024537.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00139 AC: 211AN: 152120Hom.: 2 Cov.: 33
GnomAD3 exomes AF: 0.00348 AC: 819AN: 235382Hom.: 18 AF XY: 0.00430 AC XY: 549AN XY: 127792
GnomAD4 exome AF: 0.00180 AC: 2598AN: 1442904Hom.: 51 Cov.: 30 AF XY: 0.00239 AC XY: 1715AN XY: 717370
GnomAD4 genome AF: 0.00137 AC: 209AN: 152238Hom.: 2 Cov.: 33 AF XY: 0.00172 AC XY: 128AN XY: 74460
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 05, 2016 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Combined oxidative phosphorylation defect type 27 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 28, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at