Variant rs1051740 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001136018.4(EPHX1):c.337T>C(p.Tyr113His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.278 in 151976 control chromosomes in the gnomAD Genomes database, including 6297 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.28 ( 6297 hom., cov: 32)

Exomes 𝑓: 0.32 ( 13625 hom. )

Consequence

EPHX1
NM_001136018.4 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:2O:1

Conservation

PhyloP100: 7.79

Links

EPHX1 (HGNC:3401):

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0057053864).

BP6

Variant 1-225831932-T-C is Benign according to our data. Variant chr1-225831932-T-C is described in ClinVar as [Benign]. Clinvar id is 16604. Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.434 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EPHX1	NM_001136018.4 linkuse as main transcript	c.337T>C	p.Tyr113His	missense_variant	3/9	ENST00000272167.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EPHX1	ENST00000272167.10 linkuse as main transcript	c.337T>C	p.Tyr113His	missense_variant	3/9	1	NM_001136018.4	P1

Frequencies

GnomAD3 genomes

AF:

0.278

AC:

42243

AN:

151976

Hom.:

6297

Cov.:

show subpopulations

Gnomad AFR

AF:

0.184

Gnomad AMI

AF:

0.296

Gnomad AMR

AF:

0.328

Gnomad ASJ

AF:

0.288

Gnomad EAS

AF:

0.449

Gnomad SAS

AF:

0.368

Gnomad FIN

AF:

0.297

Gnomad MID

AF:

0.244

Gnomad NFE

AF:

0.301

Gnomad OTH

AF:

0.278

GnomAD3 exomes

AF:

0.321

AC:

80762

AN:

251384

Hom.:

13625

AF XY:

0.321

AC XY:

43628

AN XY:

135882

show subpopulations

Gnomad AFR exome

AF:

0.178

Gnomad AMR exome

AF:

0.393

Gnomad ASJ exome

AF:

0.283

Gnomad EAS exome

AF:

0.461

Gnomad SAS exome

AF:

0.352

Gnomad FIN exome

AF:

0.301

Gnomad NFE exome

AF:

0.297

Gnomad OTH exome

AF:

0.307

GnomAD4 exome

AF:

0.306

AC:

447402

AN:

1461612

Hom.:

69953

AF XY:

0.307

AC XY:

223561

AN XY:

727134

show subpopulations

Gnomad4 AFR exome

AF:

0.181

Gnomad4 AMR exome

AF:

0.382

Gnomad4 ASJ exome

AF:

0.291

Gnomad4 EAS exome

AF:

0.440

Gnomad4 SAS exome

AF:

0.351

Gnomad4 FIN exome

AF:

0.298

Gnomad4 NFE exome

AF:

0.299

Gnomad4 OTH exome

AF:

0.308

Alfa

AF:

0.295

Hom.:

12549

Bravo

AF:

0.276

TwinsUK

AF:

0.293

AC:

1086

ALSPAC

AF:

0.315

AC:

1215

ESP6500AA

AF:

0.176

AC:

776

ESP6500EA

AF:

0.300

AC:

2577

ExAC

AF:

0.313

AC:

38044

Asia WGS

AF:

0.394

AC:

1370

AN:

3478

EpiCase

AF:

0.302

EpiControl

AF:

0.294

ClinVar

Significance: Benign

Submissions summary: Benign:2Other:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

EPOXIDE HYDROLASE 1 POLYMORPHISM

Benign:1

Benign, no assertion criteria provided

literature only

OMIM

Jun 01, 2001

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 10, 2018

This variant is associated with the following publications: (PMID: 23580125, 7516776, 15061915, 15355699, 22206016, 23451147, 21445251, 19952982, 8944076, 20932192, 15535985, 22610071, 19307236, 21649467, 18439551, 25087612) -

Cystic fibrosis

Other:1

risk factor, no assertion criteria provided

research

Center for Computational Genomics and Data Science, University of Alabama

Apr 01, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.42

BayesDel_addAF

Benign

-0.39

BayesDel_noAF

Benign

-0.19

Cadd

Uncertain

Dann

Uncertain

1.0

Eigen

Pathogenic

0.77

Eigen_PC

Pathogenic

0.75

FATHMM_MKL

Pathogenic

1.0

LIST_S2

Uncertain

0.95

D;.;D;D;.

MetaRNN

Benign

0.0057

T;T;T;T;T

MetaSVM

Benign

-0.89

MutationTaster

Benign

9.7e-7

P;P

PrimateAI

Uncertain

0.58

PROVEAN

Uncertain

-4.3

D;D;D;.;D

REVEL

Uncertain

0.46

Sift

Uncertain

0.012

D;D;D;.;D

Sift4G

Pathogenic

0.0

D;D;T;D;D

Polyphen

1.0

.;D;.;D;D

Vest4

0.20, 0.38, 0.22

MPC

0.86

ClinPred

0.0077

GERP RS

5.6

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.75

gMVP

0.85

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

Links

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over