chr1-53210027-A-G
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 3P and 10B. PM1PP3BP4_StrongBP6BS1BS2_Supporting
The NM_000098.3(CPT2):āc.353A>Gā(p.Asp118Gly) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000476 in 1,613,310 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. D118D) has been classified as Likely benign.
Frequency
Consequence
NM_000098.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CPT2 | NM_000098.3 | c.353A>G | p.Asp118Gly | missense_variant | 4/5 | ENST00000371486.4 | |
CPT2 | NM_001330589.2 | c.353A>G | p.Asp118Gly | missense_variant | 4/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CPT2 | ENST00000371486.4 | c.353A>G | p.Asp118Gly | missense_variant | 4/5 | 1 | NM_000098.3 | P1 | |
ENST00000629810.1 | n.591T>C | non_coding_transcript_exon_variant | 3/3 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000837 AC: 127AN: 151668Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00203 AC: 508AN: 250816Hom.: 5 AF XY: 0.00144 AC XY: 195AN XY: 135834
GnomAD4 exome AF: 0.000439 AC: 641AN: 1461524Hom.: 6 Cov.: 31 AF XY: 0.000341 AC XY: 248AN XY: 727114
GnomAD4 genome AF: 0.000837 AC: 127AN: 151786Hom.: 0 Cov.: 32 AF XY: 0.000850 AC XY: 63AN XY: 74158
ClinVar
Submissions by phenotype
not provided Uncertain:2Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Oct 25, 2016 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 30, 2018 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Nov 22, 2023 | The CPT2 c.353A>G; p.Asp118Gly variant (rs148035648), to our knowledge, is not reported in the medical literature but is reported as uncertain significance/benign in ClinVar (Variation ID: 203666). This variant is found in the Latino population with an overall allele frequency of 1.5% (505/34418 alleles, including 5 homozygotes) in the Genome Aggregation Database. The aspartic acid at codon 118 is highly conserved, and computational analyses (SIFT, PolyPhen-2) predict that this variant is deleterious. Splicing analyses (Alamut v.2.11) predict that this variant may impact splicing by creating a novel cryptic donor splice site. However, given the lack of clinical and functional data, the significance of the p.Asp118Gly variant is uncertain at this time. - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Dec 10, 2021 | - - |
CPT2-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 24, 2019 | 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). - |
Carnitine palmitoyltransferase II deficiency Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at