rs1052429
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001270454.2(WWP2):c.*1517G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.804 in 153,760 control chromosomes in the GnomAD database, including 50,160 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 0.80 ( 49678 hom., cov: 32)
Exomes 𝑓: 0.78 ( 482 hom. )
Consequence
WWP2
NM_001270454.2 3_prime_UTR
NM_001270454.2 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.36
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=-0.9).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.94 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WWP2 | NM_001270454.2 | c.*1517G>A | 3_prime_UTR_variant | 24/24 | ENST00000359154.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WWP2 | ENST00000359154.7 | c.*1517G>A | 3_prime_UTR_variant | 24/24 | 1 | NM_001270454.2 | P1 | ||
WWP2 | ENST00000356003.6 | c.*1517G>A | 3_prime_UTR_variant | 21/21 | 2 | ||||
WWP2 | ENST00000568684.1 | c.*1517G>A | 3_prime_UTR_variant | 14/14 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.804 AC: 122201AN: 152044Hom.: 49625 Cov.: 32
GnomAD3 genomes
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GnomAD4 exome AF: 0.781 AC: 1248AN: 1598Hom.: 482 Cov.: 0 AF XY: 0.788 AC XY: 662AN XY: 840
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GnomAD4 genome ? AF: 0.804 AC: 122318AN: 152162Hom.: 49678 Cov.: 32 AF XY: 0.807 AC XY: 60019AN XY: 74388
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at