16-69917388-A-G

Variant summary

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

The NM_001270454.2(WWP2):​c.1005-321A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.649 in 152,132 control chromosomes in the GnomAD database, including 32,737 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 0.65 ( 32737 hom., cov: 33)

Consequence

WWP2
NM_001270454.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0740
Variant links:
Genes affected
WWP2 (HGNC:16804): (WW domain containing E3 ubiquitin protein ligase 2) This gene encodes a member of the Nedd4 family of E3 ligases, which play an important role in protein ubiquitination. The encoded protein contains four WW domains and may play a role in multiple processes including chondrogenesis and the regulation of oncogenic signaling pathways via interactions with Smad proteins and the tumor suppressor PTEN. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene, and a pseudogene of this gene is located on the long arm of chromosome 10. [provided by RefSeq, Jul 2012]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.939 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
WWP2NM_001270454.2 linkuse as main transcriptc.1005-321A>G intron_variant ENST00000359154.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
WWP2ENST00000359154.7 linkuse as main transcriptc.1005-321A>G intron_variant 1 NM_001270454.2 P1O00308-1

Frequencies

GnomAD3 genomes
AF:
0.649
AC:
98651
AN:
152014
Hom.:
32709
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.536
Gnomad AMI
AF:
0.736
Gnomad AMR
AF:
0.694
Gnomad ASJ
AF:
0.689
Gnomad EAS
AF:
0.962
Gnomad SAS
AF:
0.751
Gnomad FIN
AF:
0.638
Gnomad MID
AF:
0.684
Gnomad NFE
AF:
0.673
Gnomad OTH
AF:
0.685
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.649
AC:
98737
AN:
152132
Hom.:
32737
Cov.:
33
AF XY:
0.652
AC XY:
48515
AN XY:
74366
show subpopulations
Gnomad4 AFR
AF:
0.536
Gnomad4 AMR
AF:
0.694
Gnomad4 ASJ
AF:
0.689
Gnomad4 EAS
AF:
0.961
Gnomad4 SAS
AF:
0.752
Gnomad4 FIN
AF:
0.638
Gnomad4 NFE
AF:
0.674
Gnomad4 OTH
AF:
0.689
Alfa
AF:
0.681
Hom.:
59475
Bravo
AF:
0.652
Asia WGS
AF:
0.830
AC:
2879
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
2.5
DANN
Benign
0.60

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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: rs904809; hg19: chr16-69951291; API