chr16-79211779-G-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_016373.4(WWOX):c.1228G>T(p.Gly410Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000279 in 1,613,942 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. G410G) has been classified as Likely benign.
Frequency
Consequence
NM_016373.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WWOX | NM_016373.4 | c.1228G>T | p.Gly410Cys | missense_variant | 9/9 | ENST00000566780.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WWOX | ENST00000566780.6 | c.1228G>T | p.Gly410Cys | missense_variant | 9/9 | 1 | NM_016373.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 152192Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.000525 AC: 130AN: 247696Hom.: 1 AF XY: 0.000631 AC XY: 85AN XY: 134674
GnomAD4 exome AF: 0.000295 AC: 431AN: 1461636Hom.: 4 Cov.: 89 AF XY: 0.000362 AC XY: 263AN XY: 727134
GnomAD4 genome AF: 0.000125 AC: 19AN: 152306Hom.: 1 Cov.: 33 AF XY: 0.000107 AC XY: 8AN XY: 74478
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2024 | WWOX: BP4, BS2 - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 29, 2021 | This variant is associated with the following publications: (PMID: 27121845) - |
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Oct 29, 2017 | - - |
Autosomal recessive spinocerebellar ataxia 12;C3463992:Developmental and epileptic encephalopathy, 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 19, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at