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GeneBe

rs2031920

Variant summary

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

The ENST00000622716.1(null):n.1173G>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 0.0334 in 152,114 control chromosomes in the GnomAD database, including 221 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as no classification for the single variant (no stars).

Frequency

Genomes: 𝑓 0.033 ( 221 hom., cov: 33)
Failed GnomAD Quality Control

Consequence


ENST00000622716.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.980
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]

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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=-0.96).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC105378575XR_946512.3 linkuse as main transcriptn.201-198G>A intron_variant, non_coding_transcript_variant
LOC105378575XR_007062396.1 linkuse as main transcriptn.619G>A non_coding_transcript_exon_variant 1/5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000622716.1 linkuse as main transcriptn.1173G>A non_coding_transcript_exon_variant 1/1
CYP2E1ENST00000463117.6 linkuse as main transcriptc.-117-455C>T intron_variant 5 P1
CYP2E1ENST00000541261.1 linkuse as main transcriptc.-117-455C>T intron_variant 4

Frequencies

GnomAD3 genomes
AF:
0.0334
AC:
5070
AN:
151996
Hom.:
215
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00759
Gnomad AMI
AF:
0.0286
Gnomad AMR
AF:
0.0875
Gnomad ASJ
AF:
0.0519
Gnomad EAS
AF:
0.204
Gnomad SAS
AF:
0.0131
Gnomad FIN
AF:
0.0218
Gnomad MID
AF:
0.00949
Gnomad NFE
AF:
0.0263
Gnomad OTH
AF:
0.0350
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AC:
0
AN:
0
Hom.:
0
Cov.:
0
AC XY:
0
AN XY:
0
GnomAD4 genome
AF:
0.0334
AC:
5082
AN:
152114
Hom.:
221
Cov.:
33
AF XY:
0.0356
AC XY:
2648
AN XY:
74368
show subpopulations
Gnomad4 AFR
AF:
0.00757
Gnomad4 AMR
AF:
0.0882
Gnomad4 ASJ
AF:
0.0519
Gnomad4 EAS
AF:
0.204
Gnomad4 SAS
AF:
0.0127
Gnomad4 FIN
AF:
0.0218
Gnomad4 NFE
AF:
0.0263
Gnomad4 OTH
AF:
0.0351
Alfa
AF:
0.0290
Hom.:
93
Bravo
AF:
0.0402
Asia WGS
AF:
0.0710
AC:
249
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
Cadd
Benign
0.22
Dann
Benign
0.30

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.

Other links and lift over

dbSNP: rs2031920; hg19: chr10-135339845; API