3-55479573-G-C
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_003392.7(WNT5A):c.141-9C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000312 in 1,570,194 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_003392.7 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
WNT5A | NM_003392.7 | c.141-9C>G | intron_variant | Intron 2 of 4 | ENST00000264634.9 | NP_003383.4 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152208Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000602 AC: 14AN: 232556Hom.: 0 AF XY: 0.0000635 AC XY: 8AN XY: 126036
GnomAD4 exome AF: 0.0000289 AC: 41AN: 1417868Hom.: 0 Cov.: 30 AF XY: 0.0000343 AC XY: 24AN XY: 699328
GnomAD4 genome AF: 0.0000525 AC: 8AN: 152326Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74490
ClinVar
Submissions by phenotype
Autosomal dominant Robinow syndrome 1 Uncertain:1
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not provided Benign:1
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WNT5A-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at