Variant rs2291635 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001979.6(EPHX2):c.1450-124G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 895,696 control chromosomes in the GnomAD database, including 5,844 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 0.12 ( 1172 hom., cov: 31)

Exomes 𝑓: 0.11 ( 4672 hom. )

Consequence

EPHX2
NM_001979.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.08

Variant links:

Genes affected

EPHX2 (HGNC:3402): (epoxide hydrolase 2) This gene encodes a member of the epoxide hydrolase family. The protein, found in both the cytosol and peroxisomes, binds to specific epoxides and converts them to the corresponding dihydrodiols. Mutations in this gene have been associated with familial hypercholesterolemia. Alternatively spliced transcript variants have been described. [provided by RefSeq, Feb 2012]

EPHX2 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=-0.92).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EPHX2	NM_001979.6 linkuse as main transcript	c.1450-124G>A		intron_variant		ENST00000521400.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EPHX2	ENST00000521400.6 linkuse as main transcript	c.1450-124G>A		intron_variant		1	NM_001979.6	P1	P34913-1

Frequencies

GnomAD3 genomes

AF:

0.120

AC:

18169

AN:

151968

Hom.:

1172

Cov.:

show subpopulations

Gnomad AFR

AF:

0.159

Gnomad AMI

AF:

0.128

Gnomad AMR

AF:

0.101

Gnomad ASJ

AF:

0.0349

Gnomad EAS

AF:

0.190

Gnomad SAS

AF:

0.120

Gnomad FIN

AF:

0.108

Gnomad MID

AF:

0.0478

Gnomad NFE

AF:

0.101

Gnomad OTH

AF:

0.0979

GnomAD4 exome

AF:

0.107

AC:

79734

AN:

743608

Hom.:

4672

AF XY:

0.106

AC XY:

40595

AN XY:

383744

show subpopulations

Gnomad4 AFR exome

AF:

0.158

Gnomad4 AMR exome

AF:

0.120

Gnomad4 ASJ exome

AF:

0.0392

Gnomad4 EAS exome

AF:

0.171

Gnomad4 SAS exome

AF:

0.108

Gnomad4 FIN exome

AF:

0.120

Gnomad4 NFE exome

AF:

0.102

Gnomad4 OTH exome

AF:

0.102

GnomAD4 genome

AF:

0.120

AC:

18180

AN:

152088

Hom.:

1172

Cov.:

AF XY:

0.119

AC XY:

8845

AN XY:

74358

show subpopulations

Gnomad4 AFR

AF:

0.159

Gnomad4 AMR

AF:

0.101

Gnomad4 ASJ

AF:

0.0349

Gnomad4 EAS

AF:

0.190

Gnomad4 SAS

AF:

0.120

Gnomad4 FIN

AF:

0.108

Gnomad4 NFE

AF:

0.101

Gnomad4 OTH

AF:

0.0964

Alfa

AF:

0.0877

Hom.:

656

Bravo

AF:

0.119

Asia WGS

AF:

0.144

AC:

501

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.29

DANN

Benign

0.65

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