rs4563403
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_018397.5(CHDH):c.*990G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 150,556 control chromosomes in the GnomAD database, including 4,828 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 0.22 ( 4828 hom., cov: 30)
Exomes 𝑓: 0.063 ( 0 hom. )
Consequence
CHDH
NM_018397.5 3_prime_UTR
NM_018397.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.201
Genes affected
CHDH (HGNC:24288): (choline dehydrogenase) The protein encoded by this gene is a choline dehydrogenase that localizes to the mitochondrion. Variations in this gene can affect susceptibility to choline deficiency. A few transcript variants have been found for this gene, but the full-length nature of only one has been characterized to date. [provided by RefSeq, Dec 2010]
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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=-0.96).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.412 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHDH | NM_018397.5 | c.*990G>A | 3_prime_UTR_variant | 9/9 | ENST00000315251.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHDH | ENST00000315251.11 | c.*990G>A | 3_prime_UTR_variant | 9/9 | 1 | NM_018397.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.216 AC: 32447AN: 150444Hom.: 4813 Cov.: 30
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GnomAD4 exome AF: 0.0625 AC: 1AN: 16Hom.: 0 Cov.: 0 AF XY: 0.100 AC XY: 1AN XY: 10
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GnomAD4 genome ? AF: 0.216 AC: 32506AN: 150540Hom.: 4828 Cov.: 30 AF XY: 0.216 AC XY: 15854AN XY: 73424
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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