chr6:32061449:A>G Detail (hg38) (TNXB)

Information

Genome

Assembly Position
hg19 chr6:32,029,226-32,029,226 View the variant detail on this assembly version.
hg38 chr6:32,061,449-32,061,449

HGVS

Type Transcript Protein
RefSeq NM_019105.6:c.7440T>C NP_061978.6:p.Tyr2480=
Ensemble ENST00000375244.7:c.7440T>C ENST00000375244.7:p.Tyr2480=
ENST00000644971.2:c.7440T>C ENST00000644971.2:p.Tyr2480=
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.659
ToMMo:0.706
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.627

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 tgv24811901 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 2018-09-19 criteria provided, single submitter not provided germline Detail
Benign 2021-09-10 criteria provided, single submitter Ehlers-Danlos syndrome due to tenascin-X deficiency 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.7440T>C (p.Tyr2480=) AND not specified ClinVar Detail
NM_001365276.2(TNXB):c.7440T>C (p.Tyr2480=) AND not provided ClinVar Detail
NM_001365276.2(TNXB):c.7440T>C (p.Tyr2480=) AND Ehlers-Danlos syndrome due to tenascin-X deficiency ClinVar Detail
NM_001365276.2(TNXB):c.7440T>C (p.Tyr2480=) AND Vesicoureteral reflux 8 ClinVar Detail
NM_001365276.2(TNXB):c.7440T>C (p.Tyr2480=) 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
rs204887 dbSNP
Genome
hg38
Position
chr6:32,061,449-32,061,449
Variant Type
snv
Reference Allele
A
Alternative Allele
G
Filtering Status (HGVD)
PASS
Filtering Status (HGVD)
VQSRTrancheSNP99.00to99.90
# of samples (HGVD)
1085
Mean of sample read depth (HGVD)
50.00
Standard deviation of sample read depth (HGVD)
24.62
Number of reference allele (HGVD)
740
Number of alternative allele (HGVD)
1430
Allele Frequency (HGVD)
0.6589861751152074
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))
rs204887
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)
8580
East Asian Allele Counts (ExAC)
5376
East Asian Heterozygous Counts (ExAC)
1976
East Asian Homozygous Counts (ExAC)
1700
East Asian Allele Frequency (ExAC)
0.6265734265734266
Chromosome Counts in All Race (ExAC)
118400
Allele Counts in All Race (ExAC)
81776
Heterozygous Counts in All Race (ExAC)
24534
Homozygous Counts in All Race (ExAC)
28621
Allele Frequency in All Race (ExAC)
0.6906756756756757
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