chr22-50570881-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_152246.3(CPT1B):c.2028+10G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00107 in 1,612,388 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00073 ( 1 hom., cov: 33)
Exomes 𝑓: 0.0011 ( 1 hom. )
Consequence
CPT1B
NM_152246.3 intron
NM_152246.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.674
Genes affected
CPT1B (HGNC:2329): (carnitine palmitoyltransferase 1B) The protein encoded by this gene, a member of the carnitine/choline acetyltransferase family, is the rate-controlling enzyme of the long-chain fatty acid beta-oxidation pathway in muscle mitochondria. This enzyme is required for the net transport of long-chain fatty acyl-CoAs from the cytoplasm into the mitochondria. Multiple transcript variants encoding different isoforms have been found for this gene, and read-through transcripts are expressed from the upstream locus that include exons from this gene. [provided by RefSeq, Jun 2009]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
?
Variant 22-50570881-C-T is Benign according to our data. Variant chr22-50570881-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3050154.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CPT1B | NM_152246.3 | c.2028+10G>A | intron_variant | ENST00000312108.12 | |||
CHKB-CPT1B | NR_027928.2 | n.3593+10G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CPT1B | ENST00000312108.12 | c.2028+10G>A | intron_variant | 1 | NM_152246.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000729 AC: 111AN: 152228Hom.: 1 Cov.: 33
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GnomAD3 exomes AF: 0.000765 AC: 190AN: 248306Hom.: 1 AF XY: 0.000743 AC XY: 100AN XY: 134544
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GnomAD4 exome AF: 0.00111 AC: 1615AN: 1460042Hom.: 1 Cov.: 32 AF XY: 0.00106 AC XY: 772AN XY: 726242
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
CPT1B-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 08, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Name
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Benign
Cadd
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Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at