rs7238
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_152246.3(CPT1B):c.*25T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 333,274 control chromosomes in the GnomAD database, including 9,182 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 0.23 ( 7377 hom., cov: 32)
Exomes 𝑓: 0.11 ( 1805 hom. )
Consequence
CPT1B
NM_152246.3 3_prime_UTR
NM_152246.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.191
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 Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.555 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CPT1B | NM_152246.3 | c.*25T>C | 3_prime_UTR_variant | 20/20 | ENST00000312108.12 | ||
CHKB-CPT1B | NR_027928.2 | n.4078T>C | non_coding_transcript_exon_variant | 30/30 | |||
LOC107985568 | XR_001755606.3 | n.1060A>G | non_coding_transcript_exon_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CPT1B | ENST00000312108.12 | c.*25T>C | 3_prime_UTR_variant | 20/20 | 1 | NM_152246.3 | P1 | ||
CPT1B | ENST00000405237.7 | c.*25T>C | 3_prime_UTR_variant | 19/19 | 1 | P1 | |||
CPT1B | ENST00000395650.6 | downstream_gene_variant | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.235 AC: 35636AN: 151860Hom.: 7355 Cov.: 32
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GnomAD4 exome AF: 0.109 AC: 19725AN: 181298Hom.: 1805 Cov.: 0 AF XY: 0.110 AC XY: 10508AN XY: 95250
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GnomAD4 genome ? AF: 0.235 AC: 35708AN: 151976Hom.: 7377 Cov.: 32 AF XY: 0.234 AC XY: 17400AN XY: 74282
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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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