chr6:32058330:C>T Detail (hg38) (TNXB)

Information

Genome

Assembly Position
hg19 chr6:32,026,107-32,026,107 View the variant detail on this assembly version.
hg38 chr6:32,058,330-32,058,330

HGVS

Type Transcript Protein
RefSeq NM_019105.6:c.7553G>A NP_061978.6:p.Gly2518Glu
Ensemble ENST00000375244.7:c.7553G>A ENST00000375244.7:p.Gly2518Glu
ENST00000644971.2:c.7553G>A ENST00000644971.2:p.Gly2518Glu
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.672
ToMMo:0.706
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.629

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 600985 OMIM
HGNC 11976 HGNC
Ensembl ENSG00000168477 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv24811782 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign criteria provided, single submitter not specified germline Detail
Benign 2021-09-10 criteria provided, multiple submitters, no conflicts Ehlers-Danlos syndrome due to tenascin-X deficiency germline unknown Detail
Benign 2018-09-07 criteria provided, single submitter not provided germline Detail
Benign 2021-09-10 criteria provided, single submitter Vesicoureteral reflux 8 germline Detail
Benign 2018-12-04 criteria provided, single submitter germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.004 schizophrenia The TDT analysis demonstrated that of the nine SNPs, three were associated with ... BeFree 14755442 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_001365276.2(TNXB):c.7553G>A (p.Gly2518Glu) AND not specified ClinVar Detail
NM_001365276.2(TNXB):c.7553G>A (p.Gly2518Glu) AND Ehlers-Danlos syndrome due to tenascin-X deficienc... ClinVar Detail
NM_001365276.2(TNXB):c.7553G>A (p.Gly2518Glu) AND not provided ClinVar Detail
NM_001365276.2(TNXB):c.7553G>A (p.Gly2518Glu) AND Vesicoureteral reflux 8 ClinVar Detail
NM_001365276.2(TNXB):c.7553G>A (p.Gly2518Glu) AND Cardiovascular phenotype ClinVar Detail
The TDT analysis demonstrated that of the nine SNPs, three were associated with schizophrenia, inclu... 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
rs1009382 dbSNP
Genome
hg38
Position
chr6:32,058,330-32,058,330
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1164
Mean of sample read depth (HGVD)
76.87
Standard deviation of sample read depth (HGVD)
35.13
Number of reference allele (HGVD)
764
Number of alternative allele (HGVD)
1564
Allele Frequency (HGVD)
0.6718213058419243
Gene Symbol (HGVD)
TNXB
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))
rs1009382
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.7061
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
11832
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16758
East Asian Chromosome Counts (ExAC)
8376
East Asian Allele Counts (ExAC)
5271
East Asian Heterozygous Counts (ExAC)
1949
East Asian Homozygous Counts (ExAC)
1661
East Asian Allele Frequency (ExAC)
0.629297994269341
Chromosome Counts in All Race (ExAC)
113514
Allele Counts in All Race (ExAC)
81641
Heterozygous Counts in All Race (ExAC)
22509
Homozygous Counts in All Race (ExAC)
29566
Allele Frequency in All Race (ExAC)
0.7192152509822577
Genome browser