chr10-133539010-A-G
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000773.4(CYP2E1):c.*46A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.757 in 1,498,996 control chromosomes in the GnomAD database, including 435,023 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 0.64 ( 33578 hom., cov: 31)
Exomes 𝑓: 0.77 ( 401445 hom. )
Consequence
CYP2E1
NM_000773.4 3_prime_UTR
NM_000773.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.276
Genes affected
CYP2E1 (HGNC:2631): (cytochrome P450 family 2 subfamily E member 1) 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 and is induced by ethanol, the diabetic state, and starvation. The enzyme metabolizes both endogenous substrates, such as ethanol, acetone, and acetal, as well as exogenous substrates including benzene, carbon tetrachloride, ethylene glycol, and nitrosamines which are premutagens found in cigarette smoke. Due to its many substrates, this enzyme may be involved in such varied processes as gluconeogenesis, hepatic cirrhosis, diabetes, and cancer. [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=-1.0).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.794 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CYP2E1 | NM_000773.4 | c.*46A>G | 3_prime_UTR_variant | 9/9 | ENST00000252945.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYP2E1 | ENST00000252945.8 | c.*46A>G | 3_prime_UTR_variant | 9/9 | 1 | NM_000773.4 | P1 | ||
CYP2E1 | ENST00000368520.1 | n.1358+1118A>G | intron_variant, non_coding_transcript_variant | 1 | |||||
CYP2E1 | ENST00000463117.6 | c.*46A>G | 3_prime_UTR_variant | 11/11 | 5 | P1 | |||
CYP2E1 | ENST00000469258.1 | n.624A>G | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.641 AC: 96946AN: 151228Hom.: 33565 Cov.: 31
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GnomAD3 exomes AF: 0.714 AC: 141380AN: 197892Hom.: 51438 AF XY: 0.724 AC XY: 77650AN XY: 107218
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GnomAD4 exome AF: 0.770 AC: 1038024AN: 1347652Hom.: 401445 Cov.: 21 AF XY: 0.769 AC XY: 510223AN XY: 663158
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GnomAD4 genome ? AF: 0.641 AC: 96977AN: 151344Hom.: 33578 Cov.: 31 AF XY: 0.639 AC XY: 47285AN XY: 73948
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ClinVar
Not reported inComputational scores
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Name
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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