1-225831554-AAAAAAG-A

Variant summary

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

The NM_001136018.4(EPHX1):c.184-219_184-214del variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.17 (1572 hom., cov: 0)
• Consequence: EPHX1 NM_001136018.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.02

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 1-225831554-AAAAAAG-A is Benign according to our data. Variant chr1-225831554-AAAAAAG-A is described in ClinVar as [Benign]. Clinvar id is 1269503.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.295 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EPHX1	NM_001136018.4	c.184-219_184-214del		intron_variant		ENST00000272167.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EPHX1	ENST00000272167.10	c.184-219_184-214del		intron_variant		1	NM_001136018.4	P1

Frequencies

GnomAD3 genomes AF: 0.166 AC: 20108 AN: 120860 Hom.: 1572 Cov.: 0

Gnomad AFR AF: 0.0728

Gnomad AMI AF: 0.108

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.0863

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.166 AC: 20106 AN: 120934 Hom.: 1572 Cov.: 0 AF XY: 0.171 AC XY: 10012 AN XY: 58660

Gnomad4 AFR AF: 0.0727

Gnomad4 AMR AF: 0.238

Gnomad4 ASJ AF: 0.201

Gnomad4 EAS AF: 0.300

Gnomad4 SAS AF: 0.310

Gnomad4 FIN AF: 0.169

Gnomad4 NFE AF: 0.187

Gnomad4 OTH AF: 0.155

Alfa AF: 0.126 Hom.: 13

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 18, 2021

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Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs200248123; hg19: chr1-226019255;