rs144601717
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_016373.4(WWOX):c.293C>T(p.Pro98Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0141 in 1,614,118 control chromosomes in the GnomAD database, including 192 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. P98P) 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 -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WWOX | NM_016373.4 | c.293C>T | p.Pro98Leu | missense_variant | 4/9 | ENST00000566780.6 | |
WWOX | NM_130791.5 | c.293C>T | p.Pro98Leu | missense_variant | 4/6 | ||
WWOX | NM_001291997.2 | c.-47C>T | 5_prime_UTR_variant | 3/8 | |||
WWOX | NR_120436.3 | n.532C>T | non_coding_transcript_exon_variant | 4/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WWOX | ENST00000566780.6 | c.293C>T | p.Pro98Leu | missense_variant | 4/9 | 1 | NM_016373.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0143 AC: 2177AN: 152118Hom.: 23 Cov.: 32
GnomAD3 exomes AF: 0.0123 AC: 3075AN: 249570Hom.: 28 AF XY: 0.0119 AC XY: 1613AN XY: 135404
GnomAD4 exome AF: 0.0141 AC: 20542AN: 1461882Hom.: 169 Cov.: 34 AF XY: 0.0138 AC XY: 10020AN XY: 727242
GnomAD4 genome ? AF: 0.0143 AC: 2179AN: 152236Hom.: 23 Cov.: 32 AF XY: 0.0134 AC XY: 1001AN XY: 74428
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 12, 2016 | 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. - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Autosomal recessive spinocerebellar ataxia 12;C3463992:Developmental and epileptic encephalopathy, 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Developmental and epileptic encephalopathy, 28 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Dec 05, 2021 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Dec 27, 2017 | - - |
Autosomal recessive spinocerebellar ataxia 12 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Dec 05, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at