rs3738042
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001136018.4(EPHX1):c.-5-3038G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 152,222 control chromosomes in the GnomAD database, including 5,103 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.25 ( 5102 hom., cov: 32)
Exomes 𝑓: 0.28 ( 1 hom. )
Consequence
EPHX1
NM_001136018.4 intron
NM_001136018.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.892
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.299 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EPHX1 | NM_001136018.4 | c.-5-3038G>A | intron_variant | ENST00000272167.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EPHX1 | ENST00000272167.10 | c.-5-3038G>A | intron_variant | 1 | NM_001136018.4 | P1 | |||
EPHX1 | ENST00000366837.5 | c.-6+143G>A | intron_variant | 1 | P1 | ||||
EPHX1 | ENST00000614058.4 | c.-5-3038G>A | intron_variant | 1 | P1 | ||||
EPHX1 | ENST00000448202.5 | c.-5-3038G>A | intron_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.248 AC: 37787AN: 152072Hom.: 5104 Cov.: 32
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GnomAD4 exome AF: 0.281 AC: 9AN: 32Hom.: 1 AF XY: 0.250 AC XY: 6AN XY: 24
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GnomAD4 genome AF: 0.248 AC: 37791AN: 152190Hom.: 5102 Cov.: 32 AF XY: 0.249 AC XY: 18504AN XY: 74398
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at