rs2860840
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000772.3(CYP2C18):c.*31C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.34 in 1,608,778 control chromosomes in the GnomAD database, including 99,437 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 0.28 ( 7353 hom., cov: 33)
Exomes 𝑓: 0.35 ( 92084 hom. )
Consequence
CYP2C18
NM_000772.3 3_prime_UTR
NM_000772.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.259
Genes affected
CYP2C18 (HGNC:2620): (cytochrome P450 family 2 subfamily C member 18) This gene encodes a member of the cytochrome P450 superfamily of enzymes. The cytochrome P450 proteins are monooxygenases which catalyze many reactions involved in drug metabolism and synthesis of cholesterol, steroids and other lipids. This protein localizes to the endoplasmic reticulum but its specific substrate has not yet been determined. The gene is located within a cluster of cytochrome P450 genes on chromosome 10q24. An additional gene, CYP2C17, was once thought to exist; however, CYP2C17 is now considered an artefact based on a chimera of CYP2C18 and CYP2C19. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
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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=-0.89).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CYP2C18 | NM_000772.3 | c.*31C>T | 3_prime_UTR_variant | 9/9 | ENST00000285979.11 | ||
CYP2C18 | NM_001128925.2 | c.*31C>T | 3_prime_UTR_variant | 8/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYP2C18 | ENST00000285979.11 | c.*31C>T | 3_prime_UTR_variant | 9/9 | 1 | NM_000772.3 | P1 | ||
CYP2C18 | ENST00000339022.6 | c.*31C>T | 3_prime_UTR_variant | 8/8 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.277 AC: 42180AN: 152020Hom.: 7342 Cov.: 33
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GnomAD3 exomes AF: 0.338 AC: 84502AN: 249938Hom.: 16291 AF XY: 0.333 AC XY: 44958AN XY: 135048
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GnomAD4 exome AF: 0.347 AC: 505120AN: 1456640Hom.: 92084 Cov.: 31 AF XY: 0.343 AC XY: 248518AN XY: 724468
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GnomAD4 genome ? AF: 0.277 AC: 42199AN: 152138Hom.: 7353 Cov.: 33 AF XY: 0.282 AC XY: 20952AN XY: 74364
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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