1-225831555-AAAAAG-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_184-215del variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.28 (2852 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 1-225831555-AAAAAG-A is Benign according to our data. Variant chr1-225831555-AAAAAG-A is described in ClinVar as [Benign]. Clinvar id is 1228965.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.362 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EPHX1	NM_001136018.4	c.184-219_184-215del		intron_variant		ENST00000272167.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EPHX1	ENST00000272167.10	c.184-219_184-215del		intron_variant		1	NM_001136018.4	P1

Frequencies

GnomAD3 genomes AF: 0.282 AC: 29039 AN: 102902 Hom.: 2847 Cov.: 0

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.173

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.282 AC: 29067 AN: 103004 Hom.: 2852 Cov.: 0 AF XY: 0.283 AC XY: 14051 AN XY: 49624

Gnomad4 AFR AF: 0.303

Gnomad4 AMR AF: 0.290

Gnomad4 ASJ AF: 0.216

Gnomad4 EAS AF: 0.382

Gnomad4 SAS AF: 0.236

Gnomad4 FIN AF: 0.277

Gnomad4 NFE AF: 0.265

Gnomad4 OTH AF: 0.262

Alfa AF: 0.172 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: rs539157916; hg19: chr1-226019256;