rs11228368
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001876.4(CPT1A):c.-13-10303T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.399 in 151,884 control chromosomes in the GnomAD database, including 14,996 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.40 ( 14996 hom., cov: 31)
Consequence
CPT1A
NM_001876.4 intron
NM_001876.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.219
Genes affected
CPT1A (HGNC:2328): (carnitine palmitoyltransferase 1A) The mitochondrial oxidation of long-chain fatty acids is initiated by the sequential action of carnitine palmitoyltransferase I (which is located in the outer membrane and is detergent-labile) and carnitine palmitoyltransferase II (which is located in the inner membrane and is detergent-stable), together with a carnitine-acylcarnitine translocase. CPT I is the key enzyme in the carnitine-dependent transport across the mitochondrial inner membrane and its deficiency results in a decreased rate of fatty acid beta-oxidation. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CPT1A | NM_001876.4 | c.-13-10303T>C | intron_variant | ENST00000265641.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CPT1A | ENST00000265641.10 | c.-13-10303T>C | intron_variant | 1 | NM_001876.4 | P1 | |||
CPT1A | ENST00000376618.6 | c.-13-10303T>C | intron_variant | 1 | |||||
CPT1A | ENST00000561996.1 | c.-13-10303T>C | intron_variant | 4 | |||||
CPT1A | ENST00000569129.5 | c.-13-10303T>C | intron_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.399 AC: 60606AN: 151766Hom.: 14997 Cov.: 31
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31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.399 AC: 60608AN: 151884Hom.: 14996 Cov.: 31 AF XY: 0.394 AC XY: 29206AN XY: 74216
GnomAD4 genome
?
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31
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29206
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74216
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818
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
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