11-68761622-G-C
Variant names:
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001876.4(CPT1A):āc.1941C>Gā(p.Ala647Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00157 in 1,614,098 control chromosomes in the GnomAD database, including 40 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.0082 ( 14 hom., cov: 31)
Exomes š: 0.00088 ( 26 hom. )
Consequence
CPT1A
NM_001876.4 synonymous
NM_001876.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.00700
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 -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.49).
BP6
Variant 11-68761622-G-C is Benign according to our data. Variant chr11-68761622-G-C is described in ClinVar as [Benign]. Clinvar id is 203653.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-0.007 with no splicing effect.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00815 (1241/152212) while in subpopulation AFR AF= 0.0279 (1160/41530). AF 95% confidence interval is 0.0266. There are 14 homozygotes in gnomad4. There are 592 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 14 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CPT1A | NM_001876.4 | c.1941C>G | p.Ala647Ala | synonymous_variant | Exon 16 of 19 | ENST00000265641.10 | NP_001867.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CPT1A | ENST00000265641.10 | c.1941C>G | p.Ala647Ala | synonymous_variant | Exon 16 of 19 | 1 | NM_001876.4 | ENSP00000265641.4 | ||
CPT1A | ENST00000376618.6 | c.1941C>G | p.Ala647Ala | synonymous_variant | Exon 16 of 19 | 1 | ENSP00000365803.2 | |||
CPT1A | ENST00000540367.5 | c.1941C>G | p.Ala647Ala | synonymous_variant | Exon 15 of 18 | 1 | ENSP00000439084.1 | |||
CPT1A | ENST00000539743.5 | c.1941C>G | p.Ala647Ala | synonymous_variant | Exon 15 of 18 | 5 | ENSP00000446108.1 |
Frequencies
GnomAD3 genomes AF: 0.00818 AC: 1244AN: 152094Hom.: 15 Cov.: 31
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GnomAD3 exomes AF: 0.00215 AC: 540AN: 251494Hom.: 14 AF XY: 0.00157 AC XY: 213AN XY: 135920
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GnomAD4 exome AF: 0.000882 AC: 1289AN: 1461886Hom.: 26 Cov.: 32 AF XY: 0.000778 AC XY: 566AN XY: 727246
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GnomAD4 genome AF: 0.00815 AC: 1241AN: 152212Hom.: 14 Cov.: 31 AF XY: 0.00796 AC XY: 592AN XY: 74414
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ClinVar
Significance: Benign
Submissions summary: Benign:6
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Carnitine palmitoyl transferase 1A deficiency Benign:3
Benign, no assertion criteria provided | clinical testing | Natera, Inc. | Sep 16, 2020 | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2025 | - - |
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Sep 21, 2023 | - - |
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 08, 2014 | 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. - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jan 31, 2017 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at