rs765277551
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_007013.4(WWP1):c.540G>A(p.Arg180Arg) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000182 in 1,540,906 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_007013.4 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
WWP1 | ENST00000517970.6 | c.540G>A | p.Arg180Arg | splice_region_variant, synonymous_variant | Exon 8 of 25 | 1 | NM_007013.4 | ENSP00000427793.1 | ||
WWP1 | ENST00000265428.4 | c.540G>A | p.Arg180Arg | splice_region_variant, synonymous_variant | Exon 6 of 23 | 1 | ENSP00000265428.4 | |||
WWP1 | ENST00000518683.5 | n.378+3381G>A | intron_variant | Intron 4 of 14 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151490Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000142 AC: 3AN: 211642Hom.: 0 AF XY: 0.0000174 AC XY: 2AN XY: 115202
GnomAD4 exome AF: 0.0000187 AC: 26AN: 1389416Hom.: 0 Cov.: 31 AF XY: 0.0000145 AC XY: 10AN XY: 689480
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151490Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 73942
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at