Variant rs2480257 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000773.4(CYP2E1):c.*41T>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 0.751 in 1,505,476 control chromosomes in the GnomAD database, including 434,684 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 0.61 ( 32429 hom., cov: 31)

Exomes 𝑓: 0.77 ( 402255 hom. )

Consequence

CYP2E1
NM_000773.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.724

Variant links:

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]

CYP2E1 links:

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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=-0.82).

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 linkuse as main transcript	c.*41T>A		3_prime_UTR_variant	9/9	ENST00000252945.8

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris
CYP2E1	ENST00000252945.8 linkuse as main transcript	c.*41T>A	3_prime_UTR_variant	9/9	1	NM_000773.4	P1
CYP2E1	ENST00000368520.1 linkuse as main transcript	n.1358+1113T>A	intron_variant, non_coding_transcript_variant		1
CYP2E1	ENST00000463117.6 linkuse as main transcript	c.*41T>A	3_prime_UTR_variant	11/11	5		P1
CYP2E1	ENST00000469258.1 linkuse as main transcript	n.619T>A	non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes

AF:

0.608

AC:

91971

AN:

151164

Hom.:

32415

Cov.:

show subpopulations

Gnomad AFR

AF:

0.209

Gnomad AMI

AF:

0.841

Gnomad AMR

AF:

0.668

Gnomad ASJ

AF:

0.730

Gnomad EAS

AF:

0.566

Gnomad SAS

AF:

0.643

Gnomad FIN

AF:

0.790

Gnomad MID

AF:

0.724

Gnomad NFE

AF:

0.799

Gnomad OTH

AF:

0.629

GnomAD3 exomes

AF:

0.705

AC:

142053

AN:

201368

Hom.:

52026

AF XY:

0.718

AC XY:

78584

AN XY:

109480

show subpopulations

Gnomad AFR exome

AF:

0.200

Gnomad AMR exome

AF:

0.671

Gnomad ASJ exome

AF:

0.734

Gnomad EAS exome

AF:

0.574

Gnomad SAS exome

AF:

0.665

Gnomad FIN exome

AF:

0.787

Gnomad NFE exome

AF:

0.800

Gnomad OTH exome

AF:

0.735

GnomAD4 exome

AF:

0.767

AC:

1038435

AN:

1354196

Hom.:

402255

Cov.:

AF XY:

0.766

AC XY:

510602

AN XY:

666218

show subpopulations

Gnomad4 AFR exome

AF:

0.196

Gnomad4 AMR exome

AF:

0.673

Gnomad4 ASJ exome

AF:

0.735

Gnomad4 EAS exome

AF:

0.562

Gnomad4 SAS exome

AF:

0.662

Gnomad4 FIN exome

AF:

0.789

Gnomad4 NFE exome

AF:

0.802

Gnomad4 OTH exome

AF:

0.728

GnomAD4 genome

AF:

0.608

AC:

91997

AN:

151280

Hom.:

32429

Cov.:

AF XY:

0.608

AC XY:

44917

AN XY:

73908

show subpopulations

Gnomad4 AFR

AF:

0.209

Gnomad4 AMR

AF:

0.667

Gnomad4 ASJ

AF:

0.730

Gnomad4 EAS

AF:

0.567

Gnomad4 SAS

AF:

0.644

Gnomad4 FIN

AF:

0.790

Gnomad4 NFE

AF:

0.799

Gnomad4 OTH

AF:

0.634

Alfa

AF:

0.698

Hom.:

6714

Asia WGS

AF:

0.616

AC:

2140

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

1.5

DANN

Benign

0.77

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over