Genetic Variant ENST00000622716.2:n.960T>C (chr10-133527044-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000622716.2(ENSG00000278518):n.960T>C 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 0.0548 in 312,078 control chromosomes in the GnomAD database, including 1,050 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 0.071 ( 695 hom., cov: 33)

Exomes 𝑓: 0.039 ( 355 hom. )

Consequence

ENSG00000278518
ENST00000622716.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.08

Publications

25 publications found

Variant links:

Genes affected

ENSG00000278518 (HGNC:):

ENSG00000278518 links:

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 was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.229 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378575	XR_007062396.1 link	n.-85T>C		upstream_gene_variant
LOC105378575	XR_946512.3 link	n.-85T>C		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	Protein
ENSG00000278518	ENST00000622716.2 link	n.960T>C	non_coding_transcript_exon_variant	Exon 1 of 1	6
CYP2E1	ENST00000463117.6 link	c.-40+171A>G	intron_variant	Intron 2 of 10	5	ENSP00000440689.1
CYP2E1	ENST00000541261.1 link	c.-40+171A>G	intron_variant	Intron 2 of 3	4	ENSP00000437799.1
ENSG00000278518	ENST00000822676.1 link	n.-55T>C	upstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.0713

AC:

10849

AN:

152060

Hom.:

692

Cov.:

show subpopulations

Gnomad AFR

AF:

0.128

Gnomad AMI

AF:

0.0504

Gnomad AMR

AF:

0.0787

Gnomad ASJ

AF:

0.0518

Gnomad EAS

AF:

0.227

Gnomad SAS

AF:

0.242

Gnomad FIN

AF:

0.0180

Gnomad MID

AF:

0.0601

Gnomad NFE

AF:

0.0206

Gnomad OTH

AF:

0.0722

GnomAD4 exome

AF:

0.0390

AC:

6240

AN:

159900

Hom.:

355

Cov.:

AF XY:

0.0402

AC XY:

3187

AN XY:

79206

show subpopulations

African (AFR)

AF:

0.127

AC:

676

AN:

5338

American (AMR)

AF:

0.0801

AC:

333

AN:

4158

Ashkenazi Jewish (ASJ)

AF:

0.0441

AC:

158

AN:

3584

East Asian (EAS)

AF:

0.230

AC:

1523

AN:

6624

South Asian (SAS)

AF:

0.189

AC:

728

AN:

3852

European-Finnish (FIN)

AF:

0.0194

AC:

AN:

4698

Middle Eastern (MID)

AF:

0.0810

AC:

AN:

568

European-Non Finnish (NFE)

AF:

0.0182

AC:

2241

AN:

123052

Other (OTH)

AF:

0.0553

AC:

444

AN:

8026

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.492

Heterozygous variant carriers

250

501

751

1002

1252

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

116

232

348

464

580

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0713

AC:

10854

AN:

152178

Hom.:

695

Cov.:

AF XY:

0.0749

AC XY:

5576

AN XY:

74422

show subpopulations

African (AFR)

AF:

0.129

AC:

5342

AN:

41454

American (AMR)

AF:

0.0785

AC:

1202

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.0518

AC:

180

AN:

3472

East Asian (EAS)

AF:

0.225

AC:

1166

AN:

5172

South Asian (SAS)

AF:

0.241

AC:

1160

AN:

4818

European-Finnish (FIN)

AF:

0.0180

AC:

191

AN:

10624

Middle Eastern (MID)

AF:

0.0544

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0206

AC:

1402

AN:

68016

Other (OTH)

AF:

0.0705

AC:

149

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

448

896

1343

1791

2239

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

128

256

384

512

640

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0439

Hom.:

729

Bravo

AF:

0.0748

Asia WGS

AF:

0.234

AC:

813

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

1.1

(source)

DANN

Benign

0.62

PhyloP100

-1.1

PromoterAI

-0.0046

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over