chr10-133528597-G-A
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_000773.4(CYP2E1):c.294G>A(p.Ser98=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000547 in 1,613,452 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0030 ( 2 hom., cov: 34)
Exomes 𝑓: 0.00030 ( 3 hom. )
Consequence
CYP2E1
NM_000773.4 synonymous
NM_000773.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.60
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 -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
?
Variant 10-133528597-G-A is Benign according to our data. Variant chr10-133528597-G-A is described in ClinVar as [Benign]. Clinvar id is 739459.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr10-133528597-G-A is described in Lovd as [Likely_benign].
BP7
?
Synonymous conserved (PhyloP=-1.6 with no splicing effect.
BS2
?
High Homozygotes in GnomAd at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CYP2E1 | NM_000773.4 | c.294G>A | p.Ser98= | synonymous_variant | 2/9 | ENST00000252945.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYP2E1 | ENST00000252945.8 | c.294G>A | p.Ser98= | synonymous_variant | 2/9 | 1 | NM_000773.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00291 AC: 443AN: 152194Hom.: 2 Cov.: 34
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GnomAD3 exomes AF: 0.000822 AC: 206AN: 250562Hom.: 0 AF XY: 0.000670 AC XY: 91AN XY: 135796
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GnomAD4 exome AF: 0.000296 AC: 432AN: 1461140Hom.: 3 Cov.: 31 AF XY: 0.000283 AC XY: 206AN XY: 726888
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 16, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
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Dann
Benign
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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