Variant 1-225844528-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_001136018.4(EPHX1):c.1071C>T(p.Asn357=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 1,614,038 control chromosomes in the GnomAD database, including 10,119 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.099 ( 851 hom., cov: 32)

Exomes 𝑓: 0.11 ( 9268 hom. )

Consequence

EPHX1
NM_001136018.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.102

Variant links:

Genes affected

EPHX1 (HGNC:3401): (epoxide hydrolase 1) Epoxide hydrolase is a critical biotransformation enzyme that converts epoxides from the degradation of aromatic compounds to trans-dihydrodiols which can be conjugated and excreted from the body. Epoxide hydrolase functions in both the activation and detoxification of epoxides. Mutations in this gene cause preeclampsia, epoxide hydrolase deficiency or increased epoxide hydrolase activity. Alternatively spliced transcript variants encoding the same protein have been found for this gene.[provided by RefSeq, Dec 2008]

EPHX1 links:

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.39).

BP6

Variant 1-225844528-C-T is Benign according to our data. Variant chr1-225844528-C-T is described in ClinVar as [Benign]. Clinvar id is 1179465.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-225844528-C-T is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=0.102 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EPHX1	NM_001136018.4 linkuse as main transcript	c.1071C>T	p.Asn357=	synonymous_variant	8/9	ENST00000272167.10	NP_001129490.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
EPHX1	ENST00000272167.10 linkuse as main transcript	c.1071C>T	p.Asn357=	synonymous_variant	8/9	1	NM_001136018.4	ENSP00000272167	P1
EPHX1	ENST00000366837.5 linkuse as main transcript	c.1071C>T	p.Asn357=	synonymous_variant	8/9	1		ENSP00000355802	P1
EPHX1	ENST00000614058.4 linkuse as main transcript	c.1071C>T	p.Asn357=	synonymous_variant	8/9	1		ENSP00000480004	P1
	ENST00000424332.1 linkuse as main transcript	n.43+1952G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes

AF:

0.0989

AC:

15037

AN:

152062

Hom.:

850

Cov.:

show subpopulations

Gnomad AFR

AF:

0.106

Gnomad AMI

AF:

0.0560

Gnomad AMR

AF:

0.0690

Gnomad ASJ

AF:

0.0810

Gnomad EAS

AF:

0.130

Gnomad SAS

AF:

0.233

Gnomad FIN

AF:

0.0567

Gnomad MID

AF:

0.108

Gnomad NFE

AF:

0.0975

Gnomad OTH

AF:

0.103

GnomAD3 exomes

AF:

0.106

AC:

26723

AN:

251446

Hom.:

1878

AF XY:

0.114

AC XY:

15525

AN XY:

135898

show subpopulations

Gnomad AFR exome

AF:

0.110

Gnomad AMR exome

AF:

0.0439

Gnomad ASJ exome

AF:

0.0678

Gnomad EAS exome

AF:

0.126

Gnomad SAS exome

AF:

0.228

Gnomad FIN exome

AF:

0.0541

Gnomad NFE exome

AF:

0.103

Gnomad OTH exome

AF:

0.0954

GnomAD4 exome

AF:

0.106

AC:

155071

AN:

1461858

Hom.:

9268

Cov.:

AF XY:

0.110

AC XY:

79966

AN XY:

727234

show subpopulations

Gnomad4 AFR exome

AF:

0.109

Gnomad4 AMR exome

AF:

0.0457

Gnomad4 ASJ exome

AF:

0.0737

Gnomad4 EAS exome

AF:

0.141

Gnomad4 SAS exome

AF:

0.224

Gnomad4 FIN exome

AF:

0.0590

Gnomad4 NFE exome

AF:

0.101

Gnomad4 OTH exome

AF:

0.104

GnomAD4 genome

AF:

0.0989

AC:

15047

AN:

152180

Hom.:

851

Cov.:

AF XY:

0.0975

AC XY:

7254

AN XY:

74392

show subpopulations

Gnomad4 AFR

AF:

0.105

Gnomad4 AMR

AF:

0.0689

Gnomad4 ASJ

AF:

0.0810

Gnomad4 EAS

AF:

0.130

Gnomad4 SAS

AF:

0.233

Gnomad4 FIN

AF:

0.0567

Gnomad4 NFE

AF:

0.0976

Gnomad4 OTH

AF:

0.106

Alfa

AF:

0.0964

Hom.:

1517

Bravo

AF:

0.0956

Asia WGS

AF:

0.161

AC:

558

AN:

3478

EpiCase

AF:

0.0959

EpiControl

AF:

0.0960

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 11, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.39

CADD

Benign

DANN

Benign

0.85

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.090

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over