NM_025216.3:c.36C>T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_025216.3(WNT10A):c.36C>T(p.Leu12Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. L12L) has been classified as Likely benign.
Frequency
Consequence
NM_025216.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
WNT10A | NM_025216.3 | c.36C>T | p.Leu12Leu | synonymous_variant | Exon 1 of 4 | ENST00000258411.8 | NP_079492.2 | |
WNT10A | XM_011511930.2 | c.36C>T | p.Leu12Leu | synonymous_variant | Exon 1 of 3 | XP_011510232.1 | ||
WNT10A | XM_011511929.3 | c.18-1130C>T | intron_variant | Intron 2 of 4 | XP_011510231.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 31
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Odonto-onycho-dermal dysplasia;C1835492:Tooth agenesis, selective, 4 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.