17-46851694-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_003396.3(WNT9B):c.56C>T(p.Ala19Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000611 in 1,309,526 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003396.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
WNT9B | NM_003396.3 | c.56C>T | p.Ala19Val | missense_variant | Exon 1 of 4 | ENST00000290015.7 | NP_003387.1 | |
WNT9B | NM_001320458.2 | c.56C>T | p.Ala19Val | missense_variant | Exon 1 of 5 | NP_001307387.1 | ||
LRRC37A2 | XM_024450773.2 | c.4810-197362C>T | intron_variant | Intron 10 of 10 | XP_024306541.1 | |||
WNT9B | XM_011525178.3 | c.95+18254C>T | intron_variant | Intron 1 of 3 | XP_011523480.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
WNT9B | ENST00000290015.7 | c.56C>T | p.Ala19Val | missense_variant | Exon 1 of 4 | 1 | NM_003396.3 | ENSP00000290015.2 | ||
WNT9B | ENST00000393461.2 | c.56C>T | p.Ala19Val | missense_variant | Exon 1 of 5 | 2 | ENSP00000377105.2 | |||
WNT9B | ENST00000575372.5 | c.95+18254C>T | intron_variant | Intron 1 of 2 | 4 | ENSP00000458192.1 |
Frequencies
GnomAD3 genomes AF: 0.0000133 AC: 2AN: 150870Hom.: 0 Cov.: 31
GnomAD4 exome AF: 0.00000518 AC: 6AN: 1158656Hom.: 0 Cov.: 31 AF XY: 0.00000891 AC XY: 5AN XY: 561104
GnomAD4 genome AF: 0.0000133 AC: 2AN: 150870Hom.: 0 Cov.: 31 AF XY: 0.0000136 AC XY: 1AN XY: 73634
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.56C>T (p.A19V) alteration is located in exon 1 (coding exon 1) of the WNT9B gene. This alteration results from a C to T substitution at nucleotide position 56, causing the alanine (A) at amino acid position 19 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at