rs9929635

chr16-79066662-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_016373.4(WWOX):c.1057-144946A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.302 in 152,142 control chromosomes in the GnomAD database, including 7,581 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 0.30 (7581 hom., cov: 33)
• Consequence: WWOX NM_016373.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.260

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.371 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WWOX	NM_016373.4	c.1057-144946A>T		intron_variant		ENST00000566780.6
WWOX	NM_001291997.2	c.718-144946A>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WWOX	ENST00000566780.6	c.1057-144946A>T		intron_variant		1	NM_016373.4	P1

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45971 AN: 152026 Hom.: 7575 Cov.: 33

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.313

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.302 AC: 45997 AN: 152142 Hom.: 7581 Cov.: 33 AF XY: 0.300 AC XY: 22316 AN XY: 74358

Gnomad4 AFR AF: 0.186

Gnomad4 AMR AF: 0.339

Gnomad4 ASJ AF: 0.315

Gnomad4 EAS AF: 0.122

Gnomad4 SAS AF: 0.179

Gnomad4 FIN AF: 0.371

Gnomad4 NFE AF: 0.375

Gnomad4 OTH AF: 0.312

Alfa AF: 0.345 Hom.: 1330

Bravo AF: 0.299

Asia WGS AF: 0.180 AC: 622 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	6.2
Dann	Benign	0.89

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

Other links and lift over

dbSNP: rs9929635; hg19: chr16-79100559;