chr19:41353016:G>A Detail (hg38) (TGFB1, TMEM91)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr19:41,858,921-41,858,921 View the variant detail on this assembly version. |
| hg38 | chr19:41,353,016-41,353,016 |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_000660.5:c.29C>T | NP_000651.3:p.Pro10Leu |
| Ensemble | ENST00000221930.6:c.29C>T | ENST00000221930.6:p.Pro10Leu |
| ENST00000600196.2:c.29C>T | ENST00000600196.2:p.Pro10Leu |
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | ||
| Ensemble | ENST00000539627.5:c.-30+1814G>A |
Summary
MGeND
| Clinical significance | |
| Variant entry | |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.542 |
| ToMMo:0.486 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.481 |
Prediction
ClinVar
| Clinical Significance |
Benign
|
| Review star |  |
| Show details | |
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
risk factor
|
2008-07-15 | no assertion criteria provided | cystic fibrosis |
germline
|
Detail |
|
risk factor
|
2008-07-15 | no assertion criteria provided | Breast cancer, invasive, susceptibility to |
germline
|
Detail |
|
Benign
|
2024-01-24 | criteria provided, multiple submitters, no conflicts | not specified |
germline
|
Detail |
|
Benign
|
2024-02-01 | criteria provided, single submitter | not provided |
germline
|
Detail |
|
Benign
|
2021-09-10 | criteria provided, single submitter | Diaphyseal dysplasia |
germline
|
Detail |
|
Benign
|
2021-09-10 | criteria provided, single submitter | Inflammatory bowel disease, immunodeficiency, and encephalopathy |
germline
|
Detail |
|
Benign
|
2021-08-11 | criteria provided, single submitter | Meckel syndrome, type 10 |
unknown
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| <0.001 | Thickening of pleura | The TIMP2 rs2277698 SNP and a haplotype consisting of the TGFB1 rs1800469 and rs... | BeFree | 24142982 | Detail |
| <0.001 | Thickening of pleura | The TIMP2 rs2277698 SNP and a haplotype consisting of the TGFB1 rs1800469 and rs... | BeFree | 24142982 | Detail |
| <0.001 | Thickening of pleura | The TIMP2 rs2277698 SNP and a haplotype consisting of the TGFB1 rs1800469 and rs... | BeFree | 24142982 | Detail |
| 0.010 | schizophrenia | This study aimed at investigating the association between schizophrenia suscepti... | BeFree | 24065520 | Detail |
| 0.027 | Malignant neoplasm of prostate | TGFB1 polymorphism L10P is not strongly associated with prostate cancer risk. | BeFree | 19039592 | Detail |
| 0.126 | Osteoporosis, Postmenopausal | We previously reported an association between the 29C>T polymorphism in the t... | BeFree | 22066986 | Detail |
| 0.009 | prostate carcinoma | TGFβ1 Leu10Pro polymorphism contributes to the development of prostate cancer: e... | BeFree | 23975370 | Detail |
| 0.090 | Malignant neoplasm of breast | The L10P polymorphism and serum levels of transforming growth factor β1 in human... | BeFree | 23887657 | Detail |
| <0.001 | stage, prostate cancer | A series of 445 consecutive patients treated for early-stage prostate cancer rec... | BeFree | 19039592 | Detail |
| 0.480 | Malignant neoplasm of breast | No association of TGFB1 L10P genotypes and breast cancer risk in BRCA1 and BRCA2... | BeFree | 18523885 | Detail |
| 0.127 | schizophrenia | This study aimed at investigating the association between schizophrenia suscepti... | BeFree | 24065520 | Detail |
| 0.019 | breast carcinoma | The L10P polymorphism and serum levels of transforming growth factor β1 in human... | BeFree | 23887657 | Detail |
| 0.027 | Malignant neoplasm of prostate | TGFβ1 Leu10Pro polymorphism contributes to the development of prostate cancer: e... | BeFree | 23975370 | Detail |
| 0.019 | breast carcinoma | TGFB1 L10P polymorphism is associated with breast cancer susceptibility: evidenc... | BeFree | 20143152 | Detail |
| 0.080 | breast carcinoma | No association of TGFB1 L10P genotypes and breast cancer risk in BRCA1 and BRCA2... | BeFree | 18523885 | Detail |
| 0.009 | prostate carcinoma | TGFB1 polymorphism L10P is not strongly associated with prostate cancer risk. | BeFree | 19039592 | Detail |
| 0.019 | breast carcinoma | Transforming growth factorβ1 L10P variant plays an active role on the breast can... | BeFree | 20349130 | Detail |
| <0.001 | Osteoarthritis of the hand | Of the SNPs, rs716508 in A2BP1 was associated with ROA (OR = 0.7, 95% CI 0.5-0.9... | BeFree | 24825461 | Detail |
| 0.123 | pulmonary emphysema | Of the genotypes examined, membership in cluster 1 (emphysema-predominant) was a... | BeFree | 20233420 | Detail |
| 0.001 | schizophrenia | This study aimed at investigating the association between schizophrenia suscepti... | BeFree | 24065520 | Detail |
| <0.001 | Osteoarthritis of distal interphalangeal joint | Of the SNPs, rs716508 in A2BP1 was associated with ROA (OR = 0.7, 95% CI 0.5-0.9... | BeFree | 24825461 | Detail |
| 0.019 | breast carcinoma | No association of TGFB1 L10P genotypes and breast cancer risk in BRCA1 and BRCA2... | BeFree | 18523885 | Detail |
| <0.001 | female breast carcinoma | Here we investigated the association of the L10P SNP with serum levels of TGFβ1 ... | BeFree | 23887657 | Detail |
| 0.019 | breast carcinoma | For five SNPs--CASP8 D302H, IGFBP3 -202 c>a, PGR V660L, SOD2 V16A, and TGFB1 ... | BeFree | 17018785 | Detail |
| 0.006 | Carcinoma of lung | Transforming growth factor-β1 rs1800470 polymorphism is associated with lung can... | BeFree | 25409890 | Detail |
| <0.001 | Restenosis | The T29C (rs1800470) polymorphism of the transforming growth factor-β1 (TGF-β1) ... | BeFree | 25449332 | Detail |
| 0.027 | Malignant neoplasm of prostate | We evaluated the influence of the TGFB1 polymorphisms by ARMS-PCR, Leu10Pro, and... | BeFree | 18058470 | Detail |
| <0.001 | aplastic anemia | Concerning TGFB1, although its polymorphisms are not related to AA susceptibilit... | BeFree | 20953611 | Detail |
| 0.360 | Malignant neoplasm of breast | No association of TGFB1 L10P genotypes and breast cancer risk in BRCA1 and BRCA2... | BeFree | 18523885 | Detail |
| <0.001 | Malignant neoplasm of female breast | Here we investigated the association of the L10P SNP with serum levels of TGFβ1 ... | BeFree | 23887657 | Detail |
| 0.020 | Malignant neoplasm of lung | Transforming growth factor-β1 rs1800470 polymorphism is associated with lung can... | BeFree | 25409890 | Detail |
| 0.001 | Moyamoya disease | As no new genetic variants were uncovered in this study of the first exon of TGF... | BeFree | 22659181 | Detail |
| <0.001 | Benign neoplasm of breast | In view of the essential role of transforming growth factorβ1 (TGFB1) on both in... | BeFree | 20349130 | Detail |
| 0.391 | cystic fibrosis | NA | CLINVAR | Detail | |
| 0.009 | prostate carcinoma | We evaluated the influence of the TGFB1 polymorphisms by ARMS-PCR, Leu10Pro, and... | BeFree | 18058470 | Detail |
| 0.080 | breast carcinoma | No association of TGFB1 L10P genotypes and breast cancer risk in BRCA1 and BRCA2... | BeFree | 18523885 | Detail |
| 0.090 | Malignant neoplasm of breast | Transforming growth factorβ1 L10P variant plays an active role on the breast can... | BeFree | 20349130 | Detail |
| 0.090 | Malignant neoplasm of breast | TGFB1 L10P polymorphism is associated with breast cancer susceptibility: evidenc... | BeFree | 20143152 | Detail |
| 0.090 | Malignant neoplasm of breast | For five SNPs--CASP8 D302H, IGFBP3 -202 c>a, PGR V660L, SOD2 V16A, and TGFB1 ... | BeFree | 17018785 | Detail |
| <0.001 | Moyamoya disease 1 | As no new genetic variants were uncovered in this study of the first exon of TGF... | BeFree | 22659181 | Detail |
| 0.090 | Malignant neoplasm of breast | No association of TGFB1 L10P genotypes and breast cancer risk in BRCA1 and BRCA2... | BeFree | 18523885 | Detail |
| 0.003 | diabetic retinopathy | This meta-analysis suggested that the +869T/C(L10P) polymorphism in TGFβ1 gene w... | BeFree | 24710116 | Detail |
| 0.490 | Camurati-Engelmann Syndrome | NA | CLINVAR | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_000660.7(TGFB1):c.29C>T (p.Pro10Leu) AND Cystic fibrosis | ClinVar | Detail |
| NM_000660.7(TGFB1):c.29C>T (p.Pro10Leu) AND Breast cancer, invasive, susceptibility to | ClinVar | Detail |
| NM_000660.7(TGFB1):c.29C>T (p.Pro10Leu) AND not specified | ClinVar | Detail |
| NM_000660.7(TGFB1):c.29C>T (p.Pro10Leu) AND not provided | ClinVar | Detail |
| NM_000660.7(TGFB1):c.29C>T (p.Pro10Leu) AND Diaphyseal dysplasia | ClinVar | Detail |
| NM_000660.7(TGFB1):c.29C>T (p.Pro10Leu) AND Inflammatory bowel disease, immunodeficiency, and enceph... | ClinVar | Detail |
| NM_000660.7(TGFB1):c.29C>T (p.Pro10Leu) AND Meckel syndrome, type 10 | ClinVar | Detail |
| The TIMP2 rs2277698 SNP and a haplotype consisting of the TGFB1 rs1800469 and rs1800470 SNPs were as... | DisGeNET | Detail |
| The TIMP2 rs2277698 SNP and a haplotype consisting of the TGFB1 rs1800469 and rs1800470 SNPs were as... | DisGeNET | Detail |
| The TIMP2 rs2277698 SNP and a haplotype consisting of the TGFB1 rs1800469 and rs1800470 SNPs were as... | DisGeNET | Detail |
| This study aimed at investigating the association between schizophrenia susceptibility and selected ... | DisGeNET | Detail |
| TGFB1 polymorphism L10P is not strongly associated with prostate cancer risk. | DisGeNET | Detail |
| We previously reported an association between the 29C>T polymorphism in the transforming growth f... | DisGeNET | Detail |
| TGFβ1 Leu10Pro polymorphism contributes to the development of prostate cancer: evidence from a meta-... | DisGeNET | Detail |
| The L10P polymorphism and serum levels of transforming growth factor β1 in human breast cancer. | DisGeNET | Detail |
| A series of 445 consecutive patients treated for early-stage prostate cancer receiving definitive I-... | DisGeNET | Detail |
| No association of TGFB1 L10P genotypes and breast cancer risk in BRCA1 and BRCA2 mutation carriers: ... | DisGeNET | Detail |
| This study aimed at investigating the association between schizophrenia susceptibility and selected ... | DisGeNET | Detail |
| The L10P polymorphism and serum levels of transforming growth factor β1 in human breast cancer. | DisGeNET | Detail |
| TGFβ1 Leu10Pro polymorphism contributes to the development of prostate cancer: evidence from a meta-... | DisGeNET | Detail |
| TGFB1 L10P polymorphism is associated with breast cancer susceptibility: evidence from a meta-analys... | DisGeNET | Detail |
| No association of TGFB1 L10P genotypes and breast cancer risk in BRCA1 and BRCA2 mutation carriers: ... | DisGeNET | Detail |
| TGFB1 polymorphism L10P is not strongly associated with prostate cancer risk. | DisGeNET | Detail |
| Transforming growth factorβ1 L10P variant plays an active role on the breast cancer susceptibility i... | DisGeNET | Detail |
| Of the SNPs, rs716508 in A2BP1 was associated with ROA (OR = 0.7, 95% CI 0.5-0.9) and rs1800470 in T... | DisGeNET | Detail |
| Of the genotypes examined, membership in cluster 1 (emphysema-predominant) was associated with TGFB1... | DisGeNET | Detail |
| This study aimed at investigating the association between schizophrenia susceptibility and selected ... | DisGeNET | Detail |
| Of the SNPs, rs716508 in A2BP1 was associated with ROA (OR = 0.7, 95% CI 0.5-0.9) and rs1800470 in T... | DisGeNET | Detail |
| No association of TGFB1 L10P genotypes and breast cancer risk in BRCA1 and BRCA2 mutation carriers: ... | DisGeNET | Detail |
| Here we investigated the association of the L10P SNP with serum levels of TGFβ1 in female breast can... | DisGeNET | Detail |
| For five SNPs--CASP8 D302H, IGFBP3 -202 c>a, PGR V660L, SOD2 V16A, and TGFB1 L10P--the associatio... | DisGeNET | Detail |
| Transforming growth factor-β1 rs1800470 polymorphism is associated with lung cancer risk: a meta-ana... | DisGeNET | Detail |
| The T29C (rs1800470) polymorphism of the transforming growth factor-β1 (TGF-β1) gene is associated w... | DisGeNET | Detail |
| We evaluated the influence of the TGFB1 polymorphisms by ARMS-PCR, Leu10Pro, and Arg25Pro, on prosta... | DisGeNET | Detail |
| Concerning TGFB1, although its polymorphisms are not related to AA susceptibility, P10L T allele (re... | DisGeNET | Detail |
| No association of TGFB1 L10P genotypes and breast cancer risk in BRCA1 and BRCA2 mutation carriers: ... | DisGeNET | Detail |
| Here we investigated the association of the L10P SNP with serum levels of TGFβ1 in female breast can... | DisGeNET | Detail |
| Transforming growth factor-β1 rs1800470 polymorphism is associated with lung cancer risk: a meta-ana... | DisGeNET | Detail |
| As no new genetic variants were uncovered in this study of the first exon of TGFB1 in European MMD p... | DisGeNET | Detail |
| In view of the essential role of transforming growth factorβ1 (TGFB1) on both inhibiting the develop... | DisGeNET | Detail |
| NA | DisGeNET | Detail |
| We evaluated the influence of the TGFB1 polymorphisms by ARMS-PCR, Leu10Pro, and Arg25Pro, on prosta... | DisGeNET | Detail |
| No association of TGFB1 L10P genotypes and breast cancer risk in BRCA1 and BRCA2 mutation carriers: ... | DisGeNET | Detail |
| Transforming growth factorβ1 L10P variant plays an active role on the breast cancer susceptibility i... | DisGeNET | Detail |
| TGFB1 L10P polymorphism is associated with breast cancer susceptibility: evidence from a meta-analys... | DisGeNET | Detail |
| For five SNPs--CASP8 D302H, IGFBP3 -202 c>a, PGR V660L, SOD2 V16A, and TGFB1 L10P--the associatio... | DisGeNET | Detail |
| As no new genetic variants were uncovered in this study of the first exon of TGFB1 in European MMD p... | DisGeNET | Detail |
| No association of TGFB1 L10P genotypes and breast cancer risk in BRCA1 and BRCA2 mutation carriers: ... | DisGeNET | Detail |
| This meta-analysis suggested that the +869T/C(L10P) polymorphism in TGFβ1 gene would be a potential ... | DisGeNET | Detail |
| NA | 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
- rs1800470 dbSNP
- Genome
- hg38
- Position
- chr19:41,353,016-41,353,016
- Variant Type
- snv
- Reference Allele
- G
- Alternative Allele
- A
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 948
- Mean of sample read depth (HGVD)
- 17.13
- Standard deviation of sample read depth (HGVD)
- 10.00
- Number of reference allele (HGVD)
- 869
- Number of alternative allele (HGVD)
- 1027
- Allele Frequency (HGVD)
- 0.5416666666666666
- Gene Symbol (HGVD)
- TGFB1
- 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))
- rs1800470
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.4863
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 8146
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16752
- East Asian Chromosome Counts (ExAC)
- 210
- East Asian Allele Counts (ExAC)
- 101
- East Asian Heterozygous Counts (ExAC)
- 53
- East Asian Homozygous Counts (ExAC)
- 24
- East Asian Allele Frequency (ExAC)
- 0.48095238095238096
- Chromosome Counts in All Race (ExAC)
- 12490
- Allele Counts in All Race (ExAC)
- 7023
- Heterozygous Counts in All Race (ExAC)
- 3155
- Homozygous Counts in All Race (ExAC)
- 1931
- Allele Frequency in All Race (ExAC)
- 0.5622898318654924
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