rs139616809
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_003392.7(WNT5A):c.140+14A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000215 in 1,537,868 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.00015 ( 1 hom., cov: 33)
Exomes 𝑓: 0.0000072 ( 0 hom. )
Consequence
WNT5A
NM_003392.7 intron
NM_003392.7 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.813
Genes affected
WNT5A (HGNC:12784): (Wnt family member 5A) The WNT gene family consists of structurally related genes which encode secreted signaling proteins. These proteins have been implicated in oncogenesis and in several developmental processes, including regulation of cell fate and patterning during embryogenesis. This gene encodes a member of the WNT family that signals through both the canonical and non-canonical WNT pathways. This protein is a ligand for the seven transmembrane receptor frizzled-5 and the tyrosine kinase orphan receptor 2. This protein plays an essential role in regulating developmental pathways during embryogenesis. This protein may also play a role in oncogenesis. Mutations in this gene are the cause of autosomal dominant Robinow syndrome. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Jan 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BP6
?
Variant 3-55480771-T-C is Benign according to our data. Variant chr3-55480771-T-C is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 160310.We mark this variant Likely_benign, oryginal submissions are: {Uncertain_significance=1, Likely_benign=1}.
BS2
?
High AC in GnomAd4 at 23 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WNT5A | NM_003392.7 | c.140+14A>G | intron_variant | ENST00000264634.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WNT5A | ENST00000264634.9 | c.140+14A>G | intron_variant | 1 | NM_003392.7 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000112 AC: 17AN: 151964Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000188 AC: 3AN: 159566Hom.: 0 AF XY: 0.0000238 AC XY: 2AN XY: 84008
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GnomAD4 exome AF: 0.00000722 AC: 10AN: 1385786Hom.: 0 Cov.: 31 AF XY: 0.00000878 AC XY: 6AN XY: 683392
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GnomAD4 genome ? AF: 0.000151 AC: 23AN: 152082Hom.: 1 Cov.: 33 AF XY: 0.000161 AC XY: 12AN XY: 74340
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:1
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
Autosomal dominant Robinow syndrome 1 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Feb 08, 2013 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 17, 2023 | - - |
Computational scores
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Name
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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