chr2:218890244:G>A Detail (hg38) (WNT10A)

Information

Genome

Assembly Position
hg19 chr2:219,754,966-219,754,966 View the variant detail on this assembly version.
hg38 chr2:218,890,244-218,890,244

HGVS

Type Transcript Protein
RefSeq NM_025216.2:c.637G>A NP_079492.2:p.Gly213Ser
Ensemble ENST00000258411.8:c.637G>A ENST00000258411.8:p.Gly213Ser
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.015
ToMMo:0.014
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.024

Prediction

ClinVar

Clinical Significance Conflicting classifications of pathogenicity
Review star
Show details
Links
Type Database ID Link
Gene MIM 606268 OMIM
HGNC 13829 HGNC
Ensembl ENSG00000135925 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv10548464 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Likely benign 2018-01-13 criteria provided, single submitter Tooth agenesis, selective, 4 germline inherited Detail
Benign 2018-01-13 criteria provided, single submitter SchC6pf-Schulz-Passarge syndrome germline Detail
Benign 2018-01-13 criteria provided, single submitter Odonto-onycho-dermal dysplasia germline inherited Detail
Conflicting interpretations of pathogenicity 2024-02-01 criteria provided, conflicting interpretations Tooth agenesis, selective, 4,Odonto-onycho-dermal dysplasia germline Detail
Conflicting interpretations of pathogenicity 2024-02-01 criteria provided, conflicting interpretations Tooth agenesis, selective, 4,Odonto-onycho-dermal dysplasia germline Detail
Uncertain significance 2014-09-15 no assertion criteria provided germline Detail
Likely pathogenic 2022-12-20 criteria provided, single submitter not provided germline Detail
Pathogenic criteria provided, single submitter Tooth agenesis, selective, 2 maternal Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.240 TOOTH AGENESIS, SELECTIVE, 4 (disorder) NA CLINVAR Detail
Annotation

Annotations

DescrptionSourceLinks
NM_025216.3(WNT10A):c.637G>A (p.Gly213Ser) AND Tooth agenesis, selective, 4 ClinVar Detail
NM_025216.3(WNT10A):c.637G>A (p.Gly213Ser) AND SchC6pf-Schulz-Passarge syndrome ClinVar Detail
NM_025216.3(WNT10A):c.637G>A (p.Gly213Ser) AND Odonto-onycho-dermal dysplasia ClinVar Detail
NM_025216.3(WNT10A):c.637G>A (p.Gly213Ser) AND multiple conditions ClinVar Detail
NM_025216.3(WNT10A):c.637G>A (p.Gly213Ser) AND multiple conditions ClinVar Detail
NM_025216.3(WNT10A):c.637G>A (p.Gly213Ser) AND Tooth agenesis ClinVar Detail
NM_025216.3(WNT10A):c.637G>A (p.Gly213Ser) AND not provided ClinVar Detail
NM_025216.3(WNT10A):c.637G>A (p.Gly213Ser) AND Tooth agenesis, selective, 2 ClinVar Detail
NA DisGeNET Detail

Overlapped Transcript Coordinates

Gene Transcript ID Exon Number Chromosome Start Stop Type Amino Mutation Transcript Position Links

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs147680216 dbSNP
Genome
hg38
Position
chr2:218,890,244-218,890,244
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1194
Mean of sample read depth (HGVD)
43.05
Standard deviation of sample read depth (HGVD)
20.67
Number of reference allele (HGVD)
2353
Number of alternative allele (HGVD)
35
Allele Frequency (HGVD)
0.014656616415410386
Gene Symbol (HGVD)
WNT10A
ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
PASS
Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
rs147680216
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0137
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
229
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8468
East Asian Allele Counts (ExAC)
201
East Asian Heterozygous Counts (ExAC)
195
East Asian Homozygous Counts (ExAC)
3
East Asian Allele Frequency (ExAC)
0.023736419461502126
Chromosome Counts in All Race (ExAC)
118674
Allele Counts in All Race (ExAC)
208
Heterozygous Counts in All Race (ExAC)
200
Homozygous Counts in All Race (ExAC)
4
Allele Frequency in All Race (ExAC)
0.0017527006758009337
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