chr11-68794820-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001876.4(CPT1A):c.863G>A(p.Arg288Gln) variant causes a missense change. The variant allele was found at a frequency of 0.007 in 1,613,936 control chromosomes in the GnomAD database, including 55 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. R288W) has been classified as Uncertain significance.
Frequency
Consequence
NM_001876.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CPT1A | NM_001876.4 | c.863G>A | p.Arg288Gln | missense_variant | 8/19 | ENST00000265641.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CPT1A | ENST00000265641.10 | c.863G>A | p.Arg288Gln | missense_variant | 8/19 | 1 | NM_001876.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00473 AC: 720AN: 152170Hom.: 2 Cov.: 33
GnomAD3 exomes AF: 0.00530 AC: 1334AN: 251488Hom.: 6 AF XY: 0.00525 AC XY: 713AN XY: 135916
GnomAD4 exome AF: 0.00723 AC: 10570AN: 1461648Hom.: 53 Cov.: 31 AF XY: 0.00689 AC XY: 5010AN XY: 727150
GnomAD4 genome AF: 0.00473 AC: 720AN: 152288Hom.: 2 Cov.: 33 AF XY: 0.00434 AC XY: 323AN XY: 74454
ClinVar
Submissions by phenotype
Carnitine palmitoyl transferase 1A deficiency Benign:4
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Dec 02, 2021 | - - |
Benign, no assertion criteria provided | clinical testing | Natera, Inc. | Sep 16, 2020 | - - |
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Aug 13, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 03, 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. - |
CPT1A-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 14, 2020 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Sep 01, 2023 | CPT1A: BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at