3-55470119-C-T
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Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_003392.7(WNT5A):c.1116G>A(p.Glu372=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,744 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 Likely benign (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Consequence
WNT5A
NM_003392.7 synonymous
NM_003392.7 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.59
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 Likely_benign. Variant got -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.37).
BP6
Variant 3-55470119-C-T is Benign according to our data. Variant chr3-55470119-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2700457.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=2.59 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
WNT5A | NM_003392.7 | c.1116G>A | p.Glu372= | synonymous_variant | 5/5 | ENST00000264634.9 | NP_003383.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
WNT5A | ENST00000264634.9 | c.1116G>A | p.Glu372= | synonymous_variant | 5/5 | 1 | NM_003392.7 | ENSP00000264634 | P1 | |
WNT5A | ENST00000474267.5 | c.1116G>A | p.Glu372= | synonymous_variant | 6/6 | 5 | ENSP00000417310 | P1 | ||
WNT5A | ENST00000497027.5 | c.1071G>A | p.Glu357= | synonymous_variant | 5/5 | 2 | ENSP00000420104 | |||
WNT5A | ENST00000493406.1 | n.23G>A | non_coding_transcript_exon_variant | 1/2 | 4 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
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GnomAD3 exomes AF: 0.00000398 AC: 1AN: 250958Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135676
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GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461744Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 727168
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GnomAD4 genome Cov.: 33
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jun 09, 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