8-86411691-A-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_007013.4(WWP1):āc.878A>Gā(p.Asn293Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,461,844 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_007013.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
WWP1 | ENST00000517970.6 | c.878A>G | p.Asn293Ser | missense_variant | Exon 9 of 25 | 1 | NM_007013.4 | ENSP00000427793.1 | ||
WWP1 | ENST00000265428.4 | c.878A>G | p.Asn293Ser | missense_variant | Exon 7 of 23 | 1 | ENSP00000265428.4 | |||
WWP1 | ENST00000518683.5 | n.532A>G | non_coding_transcript_exon_variant | Exon 5 of 15 | 1 | |||||
WWP1 | ENST00000520374.5 | n.220A>G | non_coding_transcript_exon_variant | Exon 2 of 5 | 5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251290Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135810
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461844Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 727216
GnomAD4 genome Cov.: 32
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