chr1:116235277:C>T Detail (hg19) (VANGL1)

Information

Genome

Assembly Position
hg19 chr1:116,235,277-116,235,277
hg38 chr1:115,692,656-115,692,656 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_001172411.1:c.*1277C>T
NM_138959.2:c.*1277C>T
Ensemble ENST00000369510.8:c.*1277C>T
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:0.263
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:[No Data.]

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 610132 OMIM
HGNC 15512 HGNC
Ensembl ENSG00000173218 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv2909159 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2018-01-12 criteria provided, single submitter Sacral defect with anterior meningocele germline Detail
Benign 2018-01-12 criteria provided, single submitter neural tube defect germline Detail
CIViC
[No Data.]
DisGeNET
[No Data.]
Annotation

Annotations

DescrptionSourceLinks
NM_138959.3(VANGL1):c.*1277C>T AND Sacral defect with anterior meningocele ClinVar Detail
NM_138959.3(VANGL1):c.*1277C>T AND Neural tube defect ClinVar 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
rs3204955 dbSNP
Genome
hg19
Position
chr1:116,235,277-116,235,277
Variant Type
snv
Reference Allele
C
Alternative Allele
T
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))
rs3204955
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.2629
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
4407
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
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