chr8-27516347-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001979.6(EPHX2):c.859C>T(p.Arg287Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000477 in 1,614,002 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R287Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_001979.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EPHX2 | NM_001979.6 | c.859C>T | p.Arg287Trp | missense_variant | 8/19 | ENST00000521400.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EPHX2 | ENST00000521400.6 | c.859C>T | p.Arg287Trp | missense_variant | 8/19 | 1 | NM_001979.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000224 AC: 34AN: 152064Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000111 AC: 28AN: 251470Hom.: 0 AF XY: 0.0000662 AC XY: 9AN XY: 135914
GnomAD4 exome AF: 0.0000294 AC: 43AN: 1461820Hom.: 0 Cov.: 30 AF XY: 0.0000316 AC XY: 23AN XY: 727204
GnomAD4 genome ? AF: 0.000223 AC: 34AN: 152182Hom.: 0 Cov.: 32 AF XY: 0.000161 AC XY: 12AN XY: 74408
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 15, 2023 | The c.859C>T (p.R287W) alteration is located in exon 8 (coding exon 8) of the EPHX2 gene. This alteration results from a C to T substitution at nucleotide position 859, causing the arginine (R) at amino acid position 287 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at