rs78867184

chr16-78301147-A-G

Variant summary

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

The NM_016373.4(WWOX):c.517-85713A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0479 in 152,326 control chromosomes in the GnomAD database, including 235 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 0.048 (235 hom., cov: 32)
• Consequence: WWOX NM_016373.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.20

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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0704 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WWOX	NM_016373.4	c.517-85713A>G		intron_variant		ENST00000566780.6
WWOX	NM_001291997.2	c.178-85713A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WWOX	ENST00000566780.6	c.517-85713A>G		intron_variant		1	NM_016373.4	P1

Frequencies

GnomAD3 genomes AF: 0.0479 AC: 7293 AN: 152208 Hom.: 233 Cov.: 32

Gnomad AFR AF: 0.0133

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.0371

Gnomad ASJ AF: 0.0734

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0360

Gnomad FIN AF: 0.0594

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0721

Gnomad OTH AF: 0.0588

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

GnomAD4 genome AF: 0.0479 AC: 7294 AN: 152326 Hom.: 235 Cov.: 32 AF XY: 0.0462 AC XY: 3442 AN XY: 74484

Gnomad4 AFR AF: 0.0133

Gnomad4 AMR AF: 0.0371

Gnomad4 ASJ AF: 0.0734

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0358

Gnomad4 FIN AF: 0.0594

Gnomad4 NFE AF: 0.0721

Gnomad4 OTH AF: 0.0582

Alfa AF: 0.0559 Hom.: 40

Bravo AF: 0.0460

Asia WGS AF: 0.0170 AC: 58 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	6.6
Dann	Benign	0.53

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: rs78867184; hg19: chr16-78335044;