rs2740171
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001136018.4(EPHX1):c.365-827A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.752 in 152,166 control chromosomes in the GnomAD database, including 43,472 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 0.75 ( 43472 hom., cov: 33)
Consequence
EPHX1
NM_001136018.4 intron
NM_001136018.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.90
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 was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.03).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.863 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EPHX1 | ENST00000272167.10 | c.365-827A>C | intron_variant | Intron 3 of 8 | 1 | NM_001136018.4 | ENSP00000272167.5 | |||
EPHX1 | ENST00000366837.5 | c.365-827A>C | intron_variant | Intron 3 of 8 | 1 | ENSP00000355802.4 | ||||
EPHX1 | ENST00000614058.4 | c.365-827A>C | intron_variant | Intron 3 of 8 | 1 | ENSP00000480004.1 | ||||
EPHX1 | ENST00000448202.5 | c.365-827A>C | intron_variant | Intron 3 of 3 | 2 | ENSP00000408469.1 |
Frequencies
GnomAD3 genomes AF: 0.752 AC: 114380AN: 152048Hom.: 43441 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
114380
AN:
152048
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
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Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.752 AC: 114462AN: 152166Hom.: 43472 Cov.: 33 AF XY: 0.758 AC XY: 56357AN XY: 74398 show subpopulations
GnomAD4 genome
AF:
AC:
114462
AN:
152166
Hom.:
Cov.:
33
AF XY:
AC XY:
56357
AN XY:
74398
Gnomad4 AFR
AF:
AC:
0.640629
AN:
0.640629
Gnomad4 AMR
AF:
AC:
0.807637
AN:
0.807637
Gnomad4 ASJ
AF:
AC:
0.761822
AN:
0.761822
Gnomad4 EAS
AF:
AC:
0.884541
AN:
0.884541
Gnomad4 SAS
AF:
AC:
0.847286
AN:
0.847286
Gnomad4 FIN
AF:
AC:
0.82344
AN:
0.82344
Gnomad4 NFE
AF:
AC:
0.778082
AN:
0.778082
Gnomad4 OTH
AF:
AC:
0.751185
AN:
0.751185
Heterozygous variant carriers
0
1486
2972
4457
5943
7429
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Genome Het
Genome Hom
Variant carriers
0
852
1704
2556
3408
4260
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2932
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
Mutation Taster
=100/0
polymorphism (auto)
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at