16-78386895-C-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 2P and 15B. PM2BP4_ModerateBP6_Very_StrongBP7BS1
The NM_016373.4(WWOX):c.552C>T(p.Leu184=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000209 in 1,614,114 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. L184L) has been classified as Likely benign.
Frequency
Consequence
NM_016373.4 synonymous
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.552C>T | p.Leu184= | synonymous_variant | 6/9 | ENST00000566780.6 | |
WWOX | NM_001291997.2 | c.213C>T | p.Leu71= | synonymous_variant | 5/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WWOX | ENST00000566780.6 | c.552C>T | p.Leu184= | synonymous_variant | 6/9 | 1 | NM_016373.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000283 AC: 43AN: 152178Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000301 AC: 75AN: 249382Hom.: 0 AF XY: 0.000244 AC XY: 33AN XY: 135284
GnomAD4 exome AF: 0.000202 AC: 295AN: 1461818Hom.: 1 Cov.: 34 AF XY: 0.000172 AC XY: 125AN XY: 727220
GnomAD4 genome AF: 0.000282 AC: 43AN: 152296Hom.: 0 Cov.: 32 AF XY: 0.000175 AC XY: 13AN XY: 74472
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jun 01, 2023 | WWOX: BP4, BP7 - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 28, 2020 | - - |
not specified Benign:1
Likely benign, no assertion criteria provided | clinical testing | Genetic Services Laboratory, University of Chicago | Dec 02, 2022 | - - |
Autosomal recessive spinocerebellar ataxia 12;C3463992:Developmental and epileptic encephalopathy, 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 24, 2024 | - - |
WWOX-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 31, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at