3-55470122-C-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_003392.7(WNT5A):c.1113G>A(p.Thr371Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000929 in 1,614,130 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
Consequence
NM_003392.7 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
WNT5A | NM_003392.7 | c.1113G>A | p.Thr371Thr | synonymous_variant | Exon 5 of 5 | ENST00000264634.9 | NP_003383.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
WNT5A | ENST00000264634.9 | c.1113G>A | p.Thr371Thr | synonymous_variant | Exon 5 of 5 | 1 | NM_003392.7 | ENSP00000264634.4 | ||
WNT5A | ENST00000474267.5 | c.1113G>A | p.Thr371Thr | synonymous_variant | Exon 6 of 6 | 5 | ENSP00000417310.1 | |||
WNT5A | ENST00000497027.5 | c.1068G>A | p.Thr356Thr | synonymous_variant | Exon 5 of 5 | 2 | ENSP00000420104.1 | |||
WNT5A | ENST00000493406.1 | n.20G>A | non_coding_transcript_exon_variant | Exon 1 of 2 | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152254Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000319 AC: 8AN: 250974Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135670
GnomAD4 exome AF: 0.00000889 AC: 13AN: 1461758Hom.: 0 Cov.: 30 AF XY: 0.0000151 AC XY: 11AN XY: 727172
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152372Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74520
ClinVar
Submissions by phenotype
not provided Benign:1
- -
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