rs376293017
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 4P and 10B. PM1PM2BP4_ModerateBP6_Very_Strong
The ENST00000402655.6(WWOX):c.532G>A(p.Gly178Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000247 in 1,614,080 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/15 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G178D) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000402655.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
WWOX | NM_016373.4 | c.1179G>A | p.Thr393Thr | synonymous_variant | 9/9 | ENST00000566780.6 | NP_057457.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
WWOX | ENST00000566780.6 | c.1179G>A | p.Thr393Thr | synonymous_variant | 9/9 | 1 | NM_016373.4 | ENSP00000457230.1 |
Frequencies
GnomAD3 genomes AF: 0.000204 AC: 31AN: 152200Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.000116 AC: 29AN: 249514Hom.: 0 AF XY: 0.000140 AC XY: 19AN XY: 135394
GnomAD4 exome AF: 0.000251 AC: 367AN: 1461880Hom.: 0 Cov.: 88 AF XY: 0.000232 AC XY: 169AN XY: 727240
GnomAD4 genome AF: 0.000204 AC: 31AN: 152200Hom.: 1 Cov.: 33 AF XY: 0.000121 AC XY: 9AN XY: 74354
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 04, 2017 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Autosomal recessive spinocerebellar ataxia 12;C3463992:Developmental and epileptic encephalopathy, 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 19, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at