chr16-78958895-T-A
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_016373.4(WWOX):c.1057-252713T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.53 in 152,016 control chromosomes in the GnomAD database, including 22,046 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.53 ( 22046 hom., cov: 32)
Consequence
WWOX
NM_016373.4 intron
NM_016373.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.113
Publications
2 publications found
Genes affected
WWOX (HGNC:12799): (WW domain containing oxidoreductase) This gene encodes a member of the short-chain dehydrogenases/reductases (SDR) protein family. This gene spans the FRA16D common chromosomal fragile site and appears to function as a tumor suppressor gene. Expression of the encoded protein is able to induce apoptosis, while defects in this gene are associated with multiple types of cancer. Disruption of this gene is also associated with autosomal recessive spinocerebellar ataxia 12. Disruption of a similar gene in mouse results in impaired steroidogenesis, additionally suggesting a metabolic function for the protein. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2014]
WWOX Gene-Disease associations (from GenCC):
- genetic developmental and epileptic encephalopathyInheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
- autosomal recessive spinocerebellar ataxia 12Inheritance: AR Classification: STRONG, MODERATE, SUPPORTIVE Submitted by: G2P, Labcorp Genetics (formerly Invitae), Orphanet, Ambry Genetics
- developmental and epileptic encephalopathy, 28Inheritance: AR Classification: STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), G2P, Ambry Genetics
- 46,XY partial gonadal dysgenesisInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- undetermined early-onset epileptic encephalopathyInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.888 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
WWOX | NM_016373.4 | c.1057-252713T>A | intron_variant | Intron 8 of 8 | ENST00000566780.6 | NP_057457.1 | ||
WWOX | NM_001291997.2 | c.718-252713T>A | intron_variant | Intron 7 of 7 | NP_001278926.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.530 AC: 80521AN: 151900Hom.: 22040 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
80521
AN:
151900
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.530 AC: 80567AN: 152016Hom.: 22046 Cov.: 32 AF XY: 0.536 AC XY: 39835AN XY: 74304 show subpopulations
GnomAD4 genome
AF:
AC:
80567
AN:
152016
Hom.:
Cov.:
32
AF XY:
AC XY:
39835
AN XY:
74304
show subpopulations
African (AFR)
AF:
AC:
18770
AN:
41448
American (AMR)
AF:
AC:
9333
AN:
15284
Ashkenazi Jewish (ASJ)
AF:
AC:
2361
AN:
3470
East Asian (EAS)
AF:
AC:
4706
AN:
5176
South Asian (SAS)
AF:
AC:
3131
AN:
4814
European-Finnish (FIN)
AF:
AC:
5417
AN:
10556
Middle Eastern (MID)
AF:
AC:
188
AN:
292
European-Non Finnish (NFE)
AF:
AC:
35046
AN:
67960
Other (OTH)
AF:
AC:
1180
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1873
3747
5620
7494
9367
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
712
1424
2136
2848
3560
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2601
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.