rs2070673
Positions:
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1
The ENST00000622716.1(ENSG00000278518):n.451T>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.72 in 304,230 control chromosomes in the GnomAD database, including 83,504 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 0.67 ( 38112 hom., cov: 33)
Exomes 𝑓: 0.77 ( 45392 hom. )
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.137
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.843 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ENST00000622716.1 | n.451T>A | non_coding_transcript_exon_variant | 1/1 | ||||||
CYP2E1 | ENST00000463117.6 | c.-40+190A>T | intron_variant | 5 | P1 | ||||
CYP2E1 | ENST00000541261.1 | c.-40+190A>T | intron_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.673 AC: 102273AN: 151858Hom.: 38095 Cov.: 33
GnomAD3 genomes
?
AF:
AC:
102273
AN:
151858
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.768 AC: 116879AN: 152254Hom.: 45392 Cov.: 4 AF XY: 0.769 AC XY: 58802AN XY: 76452
GnomAD4 exome
AF:
AC:
116879
AN:
152254
Hom.:
Cov.:
4
AF XY:
AC XY:
58802
AN XY:
76452
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.673 AC: 102311AN: 151976Hom.: 38112 Cov.: 33 AF XY: 0.674 AC XY: 50066AN XY: 74302
GnomAD4 genome
?
AF:
AC:
102311
AN:
151976
Hom.:
Cov.:
33
AF XY:
AC XY:
50066
AN XY:
74302
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Asia WGS
AF:
AC:
2173
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_DG_spliceai
Position offset: -2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at