rs1051740
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001136018.4(EPHX1):āc.337T>Cā(p.Tyr113His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.303 in 1,613,706 control chromosomes in the GnomAD database, including 76,258 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.28 ( 6305 hom., cov: 32)
Exomes š: 0.31 ( 69953 hom. )
Consequence
EPHX1
NM_001136018.4 missense
NM_001136018.4 missense
Scores
4
7
7
Clinical Significance
Conservation
PhyloP100: 7.79
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 -20 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.0057053864).
BP6
Variant 1-225831932-T-C is Benign according to our data. Variant chr1-225831932-T-C is described in ClinVar as [Benign]. Clinvar id is 16604.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.434 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EPHX1 | NM_001136018.4 | c.337T>C | p.Tyr113His | missense_variant | 3/9 | ENST00000272167.10 | NP_001129490.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EPHX1 | ENST00000272167.10 | c.337T>C | p.Tyr113His | missense_variant | 3/9 | 1 | NM_001136018.4 | ENSP00000272167 | P1 |
Frequencies
GnomAD3 genomes AF: 0.278 AC: 42243AN: 151976Hom.: 6297 Cov.: 32
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GnomAD3 exomes AF: 0.321 AC: 80762AN: 251384Hom.: 13625 AF XY: 0.321 AC XY: 43628AN XY: 135882
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GnomAD4 exome AF: 0.306 AC: 447402AN: 1461612Hom.: 69953 Cov.: 44 AF XY: 0.307 AC XY: 223561AN XY: 727134
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GnomAD4 genome AF: 0.278 AC: 42272AN: 152094Hom.: 6305 Cov.: 32 AF XY: 0.280 AC XY: 20809AN XY: 74322
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ClinVar
Significance: Benign
Submissions summary: Benign:3Other:1
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 10, 2018 | This variant is associated with the following publications: (PMID: 23580125, 7516776, 15061915, 15355699, 22206016, 23451147, 21445251, 19952982, 8944076, 20932192, 15535985, 22610071, 19307236, 21649467, 18439551, 25087612) - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
EPOXIDE HYDROLASE 1 POLYMORPHISM Benign:1
Benign, no assertion criteria provided | literature only | OMIM | Jun 01, 2001 | - - |
Cystic fibrosis Other:1
risk factor, no assertion criteria provided | research | Center for Computational Genomics and Data Science, University of Alabama | Apr 01, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
.;T;.;T;T
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;.;D;D;.
MetaRNN
Benign
T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
.;L;.;L;L
MutationTaster
Benign
P;P
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;D;D;.;D
REVEL
Uncertain
Sift
Uncertain
D;D;D;.;D
Sift4G
Pathogenic
D;D;T;D;D
Polyphen
1.0
.;D;.;D;D
Vest4
0.20, 0.38, 0.22
MPC
0.86
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
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