chr8-27520878-C-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBS1BS2
The NM_001979.6(EPHX2):c.946-5C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00144 in 1,614,158 control chromosomes in the GnomAD database, including 31 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_001979.6 splice_region, splice_polypyrimidine_tract, intron
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.946-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000521400.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EPHX2 | ENST00000521400.6 | c.946-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001979.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00764 AC: 1163AN: 152154Hom.: 15 Cov.: 32
GnomAD3 exomes AF: 0.00191 AC: 480AN: 251482Hom.: 8 AF XY: 0.00146 AC XY: 198AN XY: 135910
GnomAD4 exome AF: 0.000796 AC: 1163AN: 1461886Hom.: 16 Cov.: 31 AF XY: 0.000692 AC XY: 503AN XY: 727244
GnomAD4 genome ? AF: 0.00767 AC: 1168AN: 152272Hom.: 15 Cov.: 32 AF XY: 0.00708 AC XY: 527AN XY: 74460
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Aug 16, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at