chr8-27516348-G-A
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001979.6(EPHX2):c.860G>A(p.Arg287Gln) variant causes a missense change. The variant allele was found at a frequency of 0.108 in 1,613,354 control chromosomes in the GnomAD database, including 10,151 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as risk factor (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R287W) has been classified as Uncertain significance.
Frequency
Consequence
NM_001979.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EPHX2 | NM_001979.6 | c.860G>A | p.Arg287Gln | missense_variant | 8/19 | ENST00000521400.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EPHX2 | ENST00000521400.6 | c.860G>A | p.Arg287Gln | missense_variant | 8/19 | 1 | NM_001979.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.105 AC: 15880AN: 151900Hom.: 918 Cov.: 32
GnomAD3 exomes AF: 0.117 AC: 29461AN: 251406Hom.: 2087 AF XY: 0.113 AC XY: 15371AN XY: 135890
GnomAD4 exome AF: 0.109 AC: 158952AN: 1461336Hom.: 9234 Cov.: 31 AF XY: 0.108 AC XY: 78254AN XY: 726946
GnomAD4 genome ? AF: 0.105 AC: 15889AN: 152018Hom.: 917 Cov.: 32 AF XY: 0.105 AC XY: 7774AN XY: 74300
ClinVar
Submissions by phenotype
Hypercholesterolemia, familial, 1 Other:1
risk factor, no assertion criteria provided | literature only | OMIM | May 27, 2005 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at