1-225831546-CA-C

Position:

• chr1-225831546-CA-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001136018.4(EPHX1):​c.184-220del variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.16 (1030 hom., cov: 0)
• Consequence: EPHX1 NM_001136018.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.113

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 1-225831546-CA-C is Benign according to our data. Variant chr1-225831546-CA-C is described in ClinVar as [Benign]. Clinvar id is 1236761.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EPHX1	NM_001136018.4	c.184-220del		intron_variant		ENST00000272167.10	NP_001129490.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EPHX1	ENST00000272167.10	c.184-220del		intron_variant		1	NM_001136018.4	ENSP00000272167	P1

Frequencies

GnomAD3 genomes AF: 0.156 AC: 16296 AN: 104464 Hom.: 1028 Cov.: 0

Gnomad AFR AF: 0.0655

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.156

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.151

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.156 AC: 16302 AN: 104494 Hom.: 1030 Cov.: 0 AF XY: 0.157 AC XY: 7851 AN XY: 50150

Gnomad4 AFR AF: 0.0657

Gnomad4 AMR AF: 0.140

Gnomad4 ASJ AF: 0.256

Gnomad4 EAS AF: 0.212

Gnomad4 SAS AF: 0.186

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.188

Gnomad4 OTH AF: 0.152

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 19, 2021

- -

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs75126131; hg19: chr1-226019247;