chr5:82786239:C>T Detail (hg19) (VCAN)

Information

Genome

Assembly Position
hg19 chr5:82,786,239-82,786,239
hg38 chr5:83,490,420-83,490,420 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_001126336.2:c.393C>T NP_001119808.1:p.Asp131=
NM_001164098.1:c.393C>T NP_001157570.1:p.Asp131=
NM_004385.4:c.393C>T NP_004376.2:p.Asp131=
Summary

MGeND

Clinical significance Benign
Variant entry 1
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.069
ToMMo:0.078
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.067

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 118661 OMIM
HGNC 2464 HGNC
Ensembl ENSG00000038427 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv21731993 TogoVar
COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
Benign Centenarian germline MGS000068
(TMGS000140) 		Kenjiro Kosaki Keio University
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign criteria provided, single submitter not specified germline Detail
Benign 2018-01-12 criteria provided, single submitter germline Detail
Benign 2016-06-14 criteria provided, single submitter Wagner syndrome germline Detail
Benign 2024-01-31 criteria provided, multiple submitters, no conflicts not provided germline Detail
CIViC
[No Data.]
DisGeNET
[No Data.]
Annotation

Annotations

DescrptionSourceLinks
NM_004385.5(VCAN):c.393C>T (p.Asp131=) AND not specified ClinVar Detail
NM_004385.5(VCAN):c.393C>T (p.Asp131=) AND Vitreoretinopathy ClinVar Detail
NM_004385.5(VCAN):c.393C>T (p.Asp131=) AND Wagner syndrome ClinVar Detail
NM_004385.5(VCAN):c.393C>T (p.Asp131=) AND not provided 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
rs35042106 dbSNP
Genome
hg19
Position
chr5:82,786,239-82,786,239
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1158
Mean of sample read depth (HGVD)
29.07
Standard deviation of sample read depth (HGVD)
17.24
Number of reference allele (HGVD)
2156
Number of alternative allele (HGVD)
160
Allele Frequency (HGVD)
0.0690846286701209
Gene Symbol (HGVD)
VCAN
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))
rs35042106
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0783
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
1312
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8638
East Asian Allele Counts (ExAC)
582
East Asian Heterozygous Counts (ExAC)
544
East Asian Homozygous Counts (ExAC)
19
East Asian Allele Frequency (ExAC)
0.06737670757119704
Chromosome Counts in All Race (ExAC)
121328
Allele Counts in All Race (ExAC)
2993
Heterozygous Counts in All Race (ExAC)
2773
Homozygous Counts in All Race (ExAC)
110
Allele Frequency in All Race (ExAC)
0.024668666754582617
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