chr2-218881032-C-T
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_025216.3(WNT10A):c.37C>T(p.Arg13Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000011 in 1,448,006 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. R13R) has been classified as Likely benign.
Frequency
Consequence
NM_025216.3 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WNT10A | NM_025216.3 | c.37C>T | p.Arg13Ter | stop_gained | 1/4 | ENST00000258411.8 | |
WNT10A | XM_011511930.2 | c.37C>T | p.Arg13Ter | stop_gained | 1/3 | ||
WNT10A | XM_011511929.3 | c.18-1129C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WNT10A | ENST00000258411.8 | c.37C>T | p.Arg13Ter | stop_gained | 1/4 | 1 | NM_025216.3 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000928 AC: 2AN: 215480Hom.: 0 AF XY: 0.0000169 AC XY: 2AN XY: 118550
GnomAD4 exome AF: 0.0000110 AC: 16AN: 1448006Hom.: 0 Cov.: 31 AF XY: 0.00000974 AC XY: 7AN XY: 718930
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Odonto-onycho-dermal dysplasia;C1835492:Tooth agenesis, selective, 4 Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Mar 12, 2023 | For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 1916936). This variant has not been reported in the literature in individuals affected with WNT10A-related conditions. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This sequence change creates a premature translational stop signal (p.Arg13*) in the WNT10A gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in WNT10A are known to be pathogenic (PMID: 17847007, 22581971, 25629078). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at