rs147563740
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 2P and 16B. PM2BP4_StrongBP6_Very_StrongBS1
The NM_001876.4(CPT1A):c.2142+8C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000574 in 1,596,642 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001876.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CPT1A | NM_001876.4 | c.2142+8C>T | splice_region_variant, intron_variant | ENST00000265641.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CPT1A | ENST00000265641.10 | c.2142+8C>T | splice_region_variant, intron_variant | 1 | NM_001876.4 | P1 | |||
CPT1A | ENST00000376618.6 | c.2142+8C>T | splice_region_variant, intron_variant | 1 | |||||
CPT1A | ENST00000540367.5 | c.2142+8C>T | splice_region_variant, intron_variant | 1 | |||||
CPT1A | ENST00000539743.5 | c.2142+8C>T | splice_region_variant, intron_variant | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000684 AC: 104AN: 152110Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000799 AC: 187AN: 233998Hom.: 0 AF XY: 0.00101 AC XY: 128AN XY: 126274
GnomAD4 exome AF: 0.000561 AC: 811AN: 1444414Hom.: 1 Cov.: 30 AF XY: 0.000653 AC XY: 469AN XY: 717734
GnomAD4 genome ? AF: 0.000690 AC: 105AN: 152228Hom.: 0 Cov.: 32 AF XY: 0.000699 AC XY: 52AN XY: 74424
ClinVar
Submissions by phenotype
not provided Benign:3
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Likely benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2019 | - - |
Carnitine palmitoyl transferase 1A deficiency Benign:2
Likely benign, no assertion criteria provided | clinical testing | Natera, Inc. | Dec 06, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
not specified Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Aug 25, 2015 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 02, 2017 | 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
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at