rs8057659

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000566780.6(WWOX):​c.1057-241883A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.527 in 152,026 control chromosomes in the GnomAD database, including 21,239 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 ( 21239 hom., cov: 32)

Consequence

WWOX
ENST00000566780.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.718
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.545 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
WWOXNM_016373.4 linkuse as main transcriptc.1057-241883A>G intron_variant ENST00000566780.6 NP_057457.1
WWOXNM_001291997.2 linkuse as main transcriptc.718-241883A>G intron_variant NP_001278926.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
WWOXENST00000566780.6 linkuse as main transcriptc.1057-241883A>G intron_variant 1 NM_016373.4 ENSP00000457230 P1Q9NZC7-1

Frequencies

GnomAD3 genomes
AF:
0.527
AC:
80076
AN:
151908
Hom.:
21231
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.477
Gnomad AMI
AF:
0.574
Gnomad AMR
AF:
0.550
Gnomad ASJ
AF:
0.501
Gnomad EAS
AF:
0.478
Gnomad SAS
AF:
0.557
Gnomad FIN
AF:
0.558
Gnomad MID
AF:
0.532
Gnomad NFE
AF:
0.550
Gnomad OTH
AF:
0.536
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.527
AC:
80113
AN:
152026
Hom.:
21239
Cov.:
32
AF XY:
0.530
AC XY:
39378
AN XY:
74334
show subpopulations
Gnomad4 AFR
AF:
0.477
Gnomad4 AMR
AF:
0.550
Gnomad4 ASJ
AF:
0.501
Gnomad4 EAS
AF:
0.477
Gnomad4 SAS
AF:
0.558
Gnomad4 FIN
AF:
0.558
Gnomad4 NFE
AF:
0.550
Gnomad4 OTH
AF:
0.531
Alfa
AF:
0.547
Hom.:
22475
Bravo
AF:
0.521
Asia WGS
AF:
0.497
AC:
1727
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.21
DANN
Benign
0.60

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs8057659; hg19: chr16-79003622; API