chr6:31540313:A>G Detail (hg19) (LTA, LOC100287329)

Information

Genome

Assembly Position
hg19 chr6:31,540,313-31,540,313
hg38 chr6:31,572,536-31,572,536 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_000595.3:c.-10+90A>G
Ensemble ENST00000454783.5:c.-9-198A>G
ENST00000418386.3:c.-10+90A>G
Summary

MGeND

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

Frequency

JP HGVD:[No Data.]
ToMMo:0.393
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:[No Data.]

Prediction

ClinVar

Clinical Significance risk factor
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 tgv24782572 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 2004-02-15 no assertion criteria provided Psoriatic arthritis, susceptibility to germline Detail
risk factor 2004-02-15 no assertion criteria provided Myocardial infarction, susceptibility to germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
<0.001 Malignant Childhood Neoplasm We determined serum AMH levels (a marker of ovarian reserve) in adult survivors ... BeFree 23360674 Detail
<0.001 Malignant Childhood Neoplasm We determined serum AMH levels (a marker of ovarian reserve) in adult survivors ... BeFree 23360674 Detail
<0.001 Malignant Childhood Neoplasm We determined serum AMH levels (a marker of ovarian reserve) in adult survivors ... BeFree 23360674 Detail
<0.001 Malignant Childhood Neoplasm We determined serum AMH levels (a marker of ovarian reserve) in adult survivors ... BeFree 23360674 Detail
<0.001 Malignant Childhood Neoplasm We determined serum AMH levels (a marker of ovarian reserve) in adult survivors ... BeFree 23360674 Detail
<0.001 Malignant Childhood Neoplasm We determined serum AMH levels (a marker of ovarian reserve) in adult survivors ... BeFree 23360674 Detail
<0.001 Malignant Childhood Neoplasm We determined serum AMH levels (a marker of ovarian reserve) in adult survivors ... BeFree 23360674 Detail
<0.001 Respiratory syncytial virus (RSV) infection in conditions classified elsewhere and of unspecified site The following study populations were genotyped for 4 polymorphisms within TNF-be... BeFree 18811622 Detail
<0.001 bronchiolitis The following study populations were genotyped for 4 polymorphisms within TNF-be... BeFree 18811622 Detail
0.050 Lymphoma, Non-Hodgkin A haplotype comprising SNPs in two proinflammatory cytokines, tumor necrosis fac... BeFree 17018637 Detail
0.026 Lymphoma, Non-Hodgkin A haplotype comprising SNPs in two proinflammatory cytokines, tumor necrosis fac... BeFree 17018637 Detail
0.049 asthma The following study populations were genotyped for 4 polymorphisms within TNF-be... BeFree 18811622 Detail
<0.001 Ischemic stroke In the non-hypertensive group, CCL11 rs3744508, LTC4S rs730012, FCER1B rs569108,... BeFree 22769019 Detail
<0.001 Ischemic Cerebrovascular Accident In the non-hypertensive group, CCL11 rs3744508, LTC4S rs730012, FCER1B rs569108,... BeFree 22769019 Detail
0.026 Lymphoma, Non-Hodgkin Two single nucleotide polymorphisms (SNPs) in adjacent genes, lymphotoxin alpha ... BeFree 19654554 Detail
0.050 Lymphoma, Non-Hodgkin Two single nucleotide polymorphisms (SNPs) in adjacent genes, lymphotoxin alpha ... BeFree 19654554 Detail
<0.001 HIV Infections Two single nucleotide polymorphisms (SNPs) in adjacent genes, lymphotoxin alpha ... BeFree 19654554 Detail
0.008 diffuse large B-cell lymphoma Variants in TNFα (rs1800629) (GG vs. AG/AA, p &lt; 0.001) and LTA (rs909253) (AA... BeFree 23391141 Detail
0.006 diffuse large B-cell lymphoma Variants in TNFα (rs1800629) (GG vs. AG/AA, p &lt; 0.001) and LTA (rs909253) (AA... BeFree 23391141 Detail
0.006 diffuse large B-cell lymphoma Variants in TNFα (rs1800629) (GG vs. AG/AA, p &lt; 0.001) and LTA (rs909253) (AA... BeFree 23391141 Detail
0.017 stomach carcinoma Genetic Variation of BCL2 (rs2279115), NEIL2 (rs804270), LTA (rs909253), PSCA (r... BeFree 26554163 Detail
0.015 Malignant neoplasm of stomach Genetic Variation of BCL2 (rs2279115), NEIL2 (rs804270), LTA (rs909253), PSCA (r... BeFree 26554163 Detail
0.010 Malignant neoplasm of stomach Genetic Variation of BCL2 (rs2279115), NEIL2 (rs804270), LTA (rs909253), PSCA (r... BeFree 26554163 Detail
0.124 Malignant neoplasm of stomach Genetic Variation of BCL2 (rs2279115), NEIL2 (rs804270), LTA (rs909253), PSCA (r... BeFree 26554163 Detail
<0.001 Malignant neoplasm of stomach Genetic Variation of BCL2 (rs2279115), NEIL2 (rs804270), LTA (rs909253), PSCA (r... BeFree 26554163 Detail
0.010 stomach carcinoma Genetic Variation of BCL2 (rs2279115), NEIL2 (rs804270), LTA (rs909253), PSCA (r... BeFree 26554163 Detail
<0.001 stomach carcinoma Genetic Variation of BCL2 (rs2279115), NEIL2 (rs804270), LTA (rs909253), PSCA (r... BeFree 26554163 Detail
0.004 stomach carcinoma Genetic Variation of BCL2 (rs2279115), NEIL2 (rs804270), LTA (rs909253), PSCA (r... BeFree 26554163 Detail
0.003 Ovarian Failure, Premature [A large-scale candidate gene association study of age at menarche and age at na... GAD 20734064 Detail
0.002 stomach carcinoma A functional polymorphism of lymphotoxin-alpha (LTA) gene rs909253 is associated... BeFree 22748850 Detail
0.002 Delayed puberty [A large-scale candidate gene association study of age at menarche and age at na... GAD 20734064 Detail
0.002 Precocious Puberty [A large-scale candidate gene association study of age at menarche and age at na... GAD 20734064 Detail
0.120 PSORIATIC ARTHRITIS, SUSCEPTIBILITY TO (finding) NA CLINVAR Detail
0.013 polycystic ovary syndrome [A large-scale candidate gene association study of age at menarche and age at na... GAD 20734064 Detail
0.237 obesity [A large-scale candidate gene association study of age at menarche and age at na... GAD 20734064 Detail
0.005 thrombophilia [A large-scale candidate gene association study of age at menarche and age at na... GAD 20734064 Detail
0.009 uveitis [Since these variants are implicated in the susceptibility and severity of sever... GAD 20335604 Detail
0.009 Malignant neoplasm of stomach A functional polymorphism of lymphotoxin-alpha (LTA) gene rs909253 is associated... BeFree 22748850 Detail
0.002 Tobacco use disorder [A large-scale candidate gene association study of age at menarche and age at na... GAD 20734064 Detail
0.296 myocardial infarction NA CLINVAR Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000595.4(LTA):c.-10+90A>G AND Psoriatic arthritis, susceptibility to ClinVar Detail
NM_000595.4(LTA):c.-10+90A>G AND Myocardial infarction, susceptibility to ClinVar Detail
We determined serum AMH levels (a marker of ovarian reserve) in adult survivors of childhood cancer ... DisGeNET Detail
We determined serum AMH levels (a marker of ovarian reserve) in adult survivors of childhood cancer ... DisGeNET Detail
We determined serum AMH levels (a marker of ovarian reserve) in adult survivors of childhood cancer ... DisGeNET Detail
We determined serum AMH levels (a marker of ovarian reserve) in adult survivors of childhood cancer ... DisGeNET Detail
We determined serum AMH levels (a marker of ovarian reserve) in adult survivors of childhood cancer ... DisGeNET Detail
We determined serum AMH levels (a marker of ovarian reserve) in adult survivors of childhood cancer ... DisGeNET Detail
We determined serum AMH levels (a marker of ovarian reserve) in adult survivors of childhood cancer ... DisGeNET Detail
The following study populations were genotyped for 4 polymorphisms within TNF-beta (rs909253) and TN... DisGeNET Detail
The following study populations were genotyped for 4 polymorphisms within TNF-beta (rs909253) and TN... DisGeNET Detail
A haplotype comprising SNPs in two proinflammatory cytokines, tumor necrosis factor-alpha and lympho... DisGeNET Detail
A haplotype comprising SNPs in two proinflammatory cytokines, tumor necrosis factor-alpha and lympho... DisGeNET Detail
The following study populations were genotyped for 4 polymorphisms within TNF-beta (rs909253) and TN... DisGeNET Detail
In the non-hypertensive group, CCL11 rs3744508, LTC4S rs730012, FCER1B rs569108, TGFB1 rs1800469, LT... DisGeNET Detail
In the non-hypertensive group, CCL11 rs3744508, LTC4S rs730012, FCER1B rs569108, TGFB1 rs1800469, LT... DisGeNET Detail
Two single nucleotide polymorphisms (SNPs) in adjacent genes, lymphotoxin alpha (LTA +252G, rs909253... DisGeNET Detail
Two single nucleotide polymorphisms (SNPs) in adjacent genes, lymphotoxin alpha (LTA +252G, rs909253... DisGeNET Detail
Two single nucleotide polymorphisms (SNPs) in adjacent genes, lymphotoxin alpha (LTA +252G, rs909253... DisGeNET Detail
Variants in TNFα (rs1800629) (GG vs. AG/AA, p &lt; 0.001) and LTA (rs909253) (AA vs. AG/GG, p = 0.02... DisGeNET Detail
Variants in TNFα (rs1800629) (GG vs. AG/AA, p &lt; 0.001) and LTA (rs909253) (AA vs. AG/GG, p = 0.02... DisGeNET Detail
Variants in TNFα (rs1800629) (GG vs. AG/AA, p &lt; 0.001) and LTA (rs909253) (AA vs. AG/GG, p = 0.02... DisGeNET Detail
Genetic Variation of BCL2 (rs2279115), NEIL2 (rs804270), LTA (rs909253), PSCA (rs2294008) and PLCE1 ... DisGeNET Detail
Genetic Variation of BCL2 (rs2279115), NEIL2 (rs804270), LTA (rs909253), PSCA (rs2294008) and PLCE1 ... DisGeNET Detail
Genetic Variation of BCL2 (rs2279115), NEIL2 (rs804270), LTA (rs909253), PSCA (rs2294008) and PLCE1 ... DisGeNET Detail
Genetic Variation of BCL2 (rs2279115), NEIL2 (rs804270), LTA (rs909253), PSCA (rs2294008) and PLCE1 ... DisGeNET Detail
Genetic Variation of BCL2 (rs2279115), NEIL2 (rs804270), LTA (rs909253), PSCA (rs2294008) and PLCE1 ... DisGeNET Detail
Genetic Variation of BCL2 (rs2279115), NEIL2 (rs804270), LTA (rs909253), PSCA (rs2294008) and PLCE1 ... DisGeNET Detail
Genetic Variation of BCL2 (rs2279115), NEIL2 (rs804270), LTA (rs909253), PSCA (rs2294008) and PLCE1 ... DisGeNET Detail
Genetic Variation of BCL2 (rs2279115), NEIL2 (rs804270), LTA (rs909253), PSCA (rs2294008) and PLCE1 ... DisGeNET Detail
[A large-scale candidate gene association study of age at menarche and age at natural menopause.] DisGeNET Detail
A functional polymorphism of lymphotoxin-alpha (LTA) gene rs909253 is associated with gastric cancer... DisGeNET Detail
[A large-scale candidate gene association study of age at menarche and age at natural menopause.] DisGeNET Detail
[A large-scale candidate gene association study of age at menarche and age at natural menopause.] DisGeNET Detail
NA DisGeNET Detail
[A large-scale candidate gene association study of age at menarche and age at natural menopause.] DisGeNET Detail
[A large-scale candidate gene association study of age at menarche and age at natural menopause.] DisGeNET Detail
[A large-scale candidate gene association study of age at menarche and age at natural menopause.] DisGeNET Detail
[Since these variants are implicated in the susceptibility and severity of several immunologic disor... DisGeNET Detail
A functional polymorphism of lymphotoxin-alpha (LTA) gene rs909253 is associated with gastric cancer... DisGeNET Detail
[A large-scale candidate gene association study of age at menarche and age at natural menopause.] DisGeNET Detail
NA DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs909253 dbSNP
Genome
hg19
Position
chr6:31,540,313-31,540,313
Variant Type
snv
Reference Allele
A
Alternative Allele
G
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))
rs909253
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.3933
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
6592
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
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