chr6:31540784:C>A Detail (hg19) (LTA)

Information

Genome

Assembly Position
hg19 chr6:31,540,784-31,540,784
hg38 chr6:31,573,007-31,573,007 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_000595.3:c.179C>A NP_000586.2:p.Thr60Asn
Ensemble ENST00000454783.5:c.179C>A ENST00000454783.5:p.Thr60Asn
ENST00000418386.3:c.179C>A ENST00000418386.3:p.Thr60Asn
Summary

MGeND

Clinical significance not provided
Variant entry
GWAS entry 1
Disease area statistics Show details

Frequency

JP HGVD:0.403
ToMMo:0.392
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.483

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 153440 OMIM
HGNC 6709 HGNC
Ensembl ENSG00000226979 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv24782642 TogoVar
COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
not provided biliary cirrhosis, primary not provided MGS000089
(TMGS000168) 		Minoru Nakamura
Minoru Nakamura		 National Hospital Organization Nagasaki Medical Center
National Hospital Organization Nagasaki Medical Center
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
risk factor 2004-09-01 no assertion criteria provided Myocardial infarction, susceptibility to germline Detail
Benign 2019-10-16 criteria provided, single submitter LTA-related disorder germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.019 breast carcinoma Multivariate logistic regression found SNPs in genes important for T helper type... BeFree 23996684 Detail
0.031 Diabetes Mellitus, Non-Insulin-Dependent Six common genetic variants (rs2229094, rs1041981, rs1800630, rs1800629, rs36152... BeFree 20177654 Detail
0.136 colorectal cancer A further analysis revealed gender-specific effects: the TCF7L2_rs7903146_T alle... BeFree 22419714 Detail
<0.001 colorectal carcinoma A further analysis revealed gender-specific effects: the TCF7L2_rs7903146_T alle... BeFree 22419714 Detail
0.022 Metabolic syndrome X Six common genetic variants (rs2229094, rs1041981, rs1800630, rs1800629, rs36152... BeFree 20177654 Detail
0.009 Fatigue Controlling for genomic estimates of ancestry and self-reported race/ethnicity a... BeFree 24632226 Detail
0.296 myocardial infarction NA CLINVAR Detail
0.008 Cardiovascular Diseases In this clinical study, the influence of genetic variants of TNF-beta (c.7G&gt;A... BeFree 17194634 Detail
0.009 Metabolic syndrome X Six common genetic variants (rs2229094, rs1041981, rs1800630, rs1800629, rs36152... BeFree 20177654 Detail
0.011 colorectal carcinoma A further analysis revealed gender-specific effects: the TCF7L2_rs7903146_T alle... BeFree 22419714 Detail
0.007 Tuberculosis, Pulmonary Using multiple corrections, significant overall risk against PTB was observed at... BeFree 22771610 Detail
<0.001 Malignant neoplasm of breast Multivariate logistic regression found SNPs in genes important for T helper type... BeFree 23996684 Detail
0.031 Diabetes Mellitus, Non-Insulin-Dependent The common T60N polymorphism of the lymphotoxin-alpha gene is associated with ty... BeFree 15729581 Detail
0.009 Metabolic syndrome X The common T60N polymorphism of the lymphotoxin-alpha gene is associated with ty... BeFree 15729581 Detail
<0.001 breast carcinoma Multivariate logistic regression found SNPs in genes important for T helper type... BeFree 23996684 Detail
<0.001 Fatigue Controlling for genomic estimates of ancestry and self-reported race/ethnicity a... BeFree 24632226 Detail
0.090 Malignant neoplasm of breast Multivariate logistic regression found SNPs in genes important for T helper type... BeFree 23996684 Detail
<0.001 colorectal cancer A further analysis revealed gender-specific effects: the TCF7L2_rs7903146_T alle... BeFree 22419714 Detail
0.005 Malignant neoplasm of breast Multivariate logistic regression found SNPs in genes important for T helper type... BeFree 23996684 Detail
<0.001 breast carcinoma Multivariate logistic regression found SNPs in genes important for T helper type... BeFree 23996684 Detail
0.002 Fatigue Controlling for genomic estimates of ancestry and self-reported race/ethnicity a... BeFree 24632226 Detail
<0.001 Malignant neoplasm of breast Multivariate logistic regression found SNPs in genes important for T helper type... BeFree 23996684 Detail
<0.001 breast carcinoma Multivariate logistic regression found SNPs in genes important for T helper type... BeFree 23996684 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000595.4(LTA):c.179C>A (p.Thr60Asn) AND Myocardial infarction, susceptibility to ClinVar Detail
NM_000595.4(LTA):c.179C>A (p.Thr60Asn) AND LTA-related disorder ClinVar Detail
Multivariate logistic regression found SNPs in genes important for T helper type 1 (Th1) immunity (I... DisGeNET Detail
Six common genetic variants (rs2229094, rs1041981, rs1800630, rs1800629, rs361525, and rs1800610) in... DisGeNET Detail
A further analysis revealed gender-specific effects: the TCF7L2_rs7903146_T allele was associated wi... DisGeNET Detail
A further analysis revealed gender-specific effects: the TCF7L2_rs7903146_T allele was associated wi... DisGeNET Detail
Six common genetic variants (rs2229094, rs1041981, rs1800630, rs1800629, rs361525, and rs1800610) in... DisGeNET Detail
Controlling for genomic estimates of ancestry and self-reported race/ethnicity and gender, the high ... DisGeNET Detail
NA DisGeNET Detail
In this clinical study, the influence of genetic variants of TNF-beta (c.7G&gt;A, IVS1+90G&gt;A, C13... DisGeNET Detail
Six common genetic variants (rs2229094, rs1041981, rs1800630, rs1800629, rs361525, and rs1800610) in... DisGeNET Detail
A further analysis revealed gender-specific effects: the TCF7L2_rs7903146_T allele was associated wi... DisGeNET Detail
Using multiple corrections, significant overall risk against PTB was observed at seven loci which in... DisGeNET Detail
Multivariate logistic regression found SNPs in genes important for T helper type 1 (Th1) immunity (I... DisGeNET Detail
The common T60N polymorphism of the lymphotoxin-alpha gene is associated with type 2 diabetes and ot... DisGeNET Detail
The common T60N polymorphism of the lymphotoxin-alpha gene is associated with type 2 diabetes and ot... DisGeNET Detail
Multivariate logistic regression found SNPs in genes important for T helper type 1 (Th1) immunity (I... DisGeNET Detail
Controlling for genomic estimates of ancestry and self-reported race/ethnicity and gender, the high ... DisGeNET Detail
Multivariate logistic regression found SNPs in genes important for T helper type 1 (Th1) immunity (I... DisGeNET Detail
A further analysis revealed gender-specific effects: the TCF7L2_rs7903146_T allele was associated wi... DisGeNET Detail
Multivariate logistic regression found SNPs in genes important for T helper type 1 (Th1) immunity (I... DisGeNET Detail
Multivariate logistic regression found SNPs in genes important for T helper type 1 (Th1) immunity (I... DisGeNET Detail
Controlling for genomic estimates of ancestry and self-reported race/ethnicity and gender, the high ... DisGeNET Detail
Multivariate logistic regression found SNPs in genes important for T helper type 1 (Th1) immunity (I... DisGeNET Detail
Multivariate logistic regression found SNPs in genes important for T helper type 1 (Th1) immunity (I... 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
rs1041981 dbSNP
Genome
hg19
Position
chr6:31,540,784-31,540,784
Variant Type
snv
Reference Allele
C
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1166
Mean of sample read depth (HGVD)
203.83
Standard deviation of sample read depth (HGVD)
87.17
Number of reference allele (HGVD)
1392
Number of alternative allele (HGVD)
939
Allele Frequency (HGVD)
0.40283140283140284
Gene Symbol (HGVD)
LTA
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))
rs1041981
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.3923
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
6574
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16758
East Asian Chromosome Counts (ExAC)
8478
East Asian Allele Counts (ExAC)
4097
East Asian Heterozygous Counts (ExAC)
2137
East Asian Homozygous Counts (ExAC)
980
East Asian Allele Frequency (ExAC)
0.4832507666902571
Chromosome Counts in All Race (ExAC)
116668
Allele Counts in All Race (ExAC)
40788
Heterozygous Counts in All Race (ExAC)
26118
Homozygous Counts in All Race (ExAC)
7335
Allele Frequency in All Race (ExAC)
0.3496074330579079
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