rs2031920

Variant summary

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

The ENST00000622716(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 151996 control chromosomes in the gnomAD Genomes database, including 215 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as no interpretation for the single variant (no stars).

Frequency

Genomes: 𝑓 0.033 ( 215 hom., cov: 33)

Consequence

ENST00000622716 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.980

Links

(HGNC:):

CYP2E1 (HGNC:2631):

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

GnomAd 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
LOC105378575	XR_946512.3 linkuse as main transcript	n.201-198G>A		intron_variant, non_coding_transcript_variant
LOC105378575	XR_007062396.1 linkuse as main transcript	n.619G>A		non_coding_transcript_exon_variant	1/5

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	Appris
	ENST00000622716.1 linkuse as main transcript	n.1173G>A	non_coding_transcript_exon_variant	1/1
CYP2E1	ENST00000463117.6 linkuse as main transcript	c.-117-455C>T	intron_variant		5	P1
CYP2E1	ENST00000541261.1 linkuse as main transcript	c.-117-455C>T	intron_variant		4

Frequencies

GnomAD3 genomes

AF:

0.0334

AC:

5070

AN:

151996

Hom.:

215

Cov.:

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

Alfa

AF:

0.0290

Hom.:

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

0.14

Dann

Benign

0.30

Splicing

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

Links

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over