NM_003396.3:c.317T>G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_003396.3(WNT9B):āc.317T>Gā(p.Met106Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M106T) has been classified as Likely benign.
Frequency
Consequence
NM_003396.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
WNT9B | NM_003396.3 | c.317T>G | p.Met106Arg | missense_variant | Exon 2 of 4 | ENST00000290015.7 | NP_003387.1 | |
WNT9B | NM_001320458.2 | c.317T>G | p.Met106Arg | missense_variant | Exon 2 of 5 | NP_001307387.1 | ||
WNT9B | XM_011525178.3 | c.335T>G | p.Met112Arg | missense_variant | Exon 2 of 4 | XP_011523480.1 | ||
LRRC37A2 | XM_024450773.2 | c.4810-176300T>G | intron_variant | Intron 10 of 10 | XP_024306541.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
WNT9B | ENST00000290015.7 | c.317T>G | p.Met106Arg | missense_variant | Exon 2 of 4 | 1 | NM_003396.3 | ENSP00000290015.2 | ||
WNT9B | ENST00000393461.2 | c.317T>G | p.Met106Arg | missense_variant | Exon 2 of 5 | 2 | ENSP00000377105.2 | |||
WNT9B | ENST00000575372.5 | c.335T>G | p.Met112Arg | missense_variant | Exon 2 of 3 | 4 | ENSP00000458192.1 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 149824Hom.: 0 Cov.: 26 FAILED QC
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1441200Hom.: 0 Cov.: 57 AF XY: 0.00 AC XY: 0AN XY: 716438
GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 149824Hom.: 0 Cov.: 26 AF XY: 0.00 AC XY: 0AN XY: 73006
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at