rs802024
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_021151.4(CROT):c.116-2803C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.049 in 152,134 control chromosomes in the GnomAD database, including 232 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 0.049 ( 232 hom., cov: 32)
Consequence
CROT
NM_021151.4 intron
NM_021151.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.736
Genes affected
CROT (HGNC:2366): (carnitine O-octanoyltransferase) This gene encodes a member of the carnitine/choline acetyltransferase family. The encoded protein converts 4,8-dimethylnonanoyl-CoA to its corresponding carnitine ester. This transesterification occurs in the peroxisome and is necessary for transport of medium- and long- chain acyl-CoA molecules out of the peroxisome to the cytosol and mitochondria. The protein thus plays a role in lipid metabolism and fatty acid beta-oxidation. Alternatively spliced transcript variants have been described.[provided by RefSeq, Jan 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=-0.92).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0558 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CROT | NM_021151.4 | c.116-2803C>T | intron_variant | ENST00000331536.8 | |||
CROT | NM_001143935.2 | c.116-1104C>T | intron_variant | ||||
CROT | NM_001243745.3 | c.116-2803C>T | intron_variant | ||||
CROT | XM_011516337.4 | c.116-2803C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CROT | ENST00000331536.8 | c.116-2803C>T | intron_variant | 1 | NM_021151.4 | P1 | |||
CROT | ENST00000412227.6 | c.116-2803C>T | intron_variant | 1 | |||||
CROT | ENST00000419147.6 | c.116-1104C>T | intron_variant | 2 | |||||
CROT | ENST00000442291.1 | c.116-2803C>T | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0489 AC: 7439AN: 152016Hom.: 231 Cov.: 32
GnomAD3 genomes
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0490 AC: 7448AN: 152134Hom.: 232 Cov.: 32 AF XY: 0.0484 AC XY: 3600AN XY: 74370
GnomAD4 genome
?
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152134
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32
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74370
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
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