rs192779168
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6BP7
The NM_000098.3(CPT2):c.1422C>A(p.Ala474=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000378 in 1,614,120 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.00022 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000018 ( 0 hom. )
Consequence
CPT2
NM_000098.3 synonymous
NM_000098.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.150
Genes affected
CPT2 (HGNC:2330): (carnitine palmitoyltransferase 2) The protein encoded by this gene is a nuclear protein which is transported to the mitochondrial inner membrane. Together with carnitine palmitoyltransferase I, the encoded protein oxidizes long-chain fatty acids in the mitochondria. Defects in this gene are associated with mitochondrial long-chain fatty-acid (LCFA) oxidation disorders. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.34).
BP6
?
Variant 1-53211096-C-A is Benign according to our data. Variant chr1-53211096-C-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 385445.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=3, Uncertain_significance=1}.
BP7
?
Synonymous conserved (PhyloP=0.15 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CPT2 | NM_000098.3 | c.1422C>A | p.Ala474= | synonymous_variant | 4/5 | ENST00000371486.4 | |
CPT2 | NM_001330589.2 | c.1422C>A | p.Ala474= | synonymous_variant | 4/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CPT2 | ENST00000371486.4 | c.1422C>A | p.Ala474= | synonymous_variant | 4/5 | 1 | NM_000098.3 | P1 | |
ENST00000629810.1 | n.286-687G>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000223 AC: 34AN: 152208Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000558 AC: 14AN: 251028Hom.: 0 AF XY: 0.0000516 AC XY: 7AN XY: 135730
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GnomAD4 exome AF: 0.0000185 AC: 27AN: 1461794Hom.: 0 Cov.: 34 AF XY: 0.0000179 AC XY: 13AN XY: 727192
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GnomAD4 genome ? AF: 0.000223 AC: 34AN: 152326Hom.: 0 Cov.: 32 AF XY: 0.000295 AC XY: 22AN XY: 74494
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:4
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
not provided Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jan 16, 2017 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Mar 05, 2018 | - - |
Carnitine palmitoyltransferase II deficiency Benign:2
Likely benign, no assertion criteria provided | clinical testing | Natera, Inc. | Apr 30, 2020 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 21, 2024 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 25, 2018 | 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. - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at