chr19:17389704:G>A Detail (hg19) (BABAM1)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr19:17,389,704-17,389,704 |
| hg38 | chr19:17,278,895-17,278,895 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_001033549.2:c.837G>A | NP_001028721.1:p.Lys279= |
| NM_001288757.1:c.612G>A | NP_001275686.1:p.Lys204= | |
| NM_001288756.1:c.837G>A | NP_001275685.1:p.Lys279= |
Summary
MGeND
| Clinical significance | |
| Variant entry | |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:<0.001 |
| ToMMo:<0.001 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:<0.001 |
Prediction
ClinVar
| Clinical Significance | |
| Review star | [No Data.] |
| Show details | |
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
[No Data.]
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.017 | breast carcinoma | Ten SNPs (rs2075555 in COL1A1, rs12652447 in FBXL17, rs10941679 in 5p12/MRPS30, ... | BeFree | 24528085 | Detail |
| 0.026 | Malignant neoplasm of breast | Ten SNPs (rs2075555 in COL1A1, rs12652447 in FBXL17, rs10941679 in 5p12/MRPS30, ... | BeFree | 24528085 | Detail |
| 0.024 | Triple Negative Breast Neoplasms | We identified six single-nucleotide polymorphisms, including rs2046210 (ESR1), r... | BeFree | 21844186 | Detail |
| <0.001 | Triple Negative Breast Neoplasms | We identified six single-nucleotide polymorphisms, including rs2046210 (ESR1), r... | BeFree | 21844186 | Detail |
| <0.001 | Triple Negative Breast Neoplasms | We identified six single-nucleotide polymorphisms, including rs2046210 (ESR1), r... | BeFree | 21844186 | Detail |
| 0.121 | Malignant neoplasm of breast | Seven SNPs were statistically significant (P ≤ 0.05) with the risk of overall br... | BeFree | 23593120 | Detail |
| 0.002 | breast carcinoma | Seven SNPs were statistically significant (P ≤ 0.05) with the risk of overall br... | BeFree | 23593120 | Detail |
| 0.003 | breast carcinoma | Seven SNPs were statistically significant (P ≤ 0.05) with the risk of overall br... | BeFree | 23593120 | Detail |
| 0.080 | breast carcinoma | Index SNPs in five loci were replicated, including three associated with ER-/PR-... | BeFree | 23136140 | Detail |
| <0.001 | breast carcinoma | Seven SNPs were statistically significant (P ≤ 0.05) with the risk of overall br... | BeFree | 23593120 | Detail |
| 0.031 | breast carcinoma | Seven SNPs were statistically significant (P ≤ 0.05) with the risk of overall br... | BeFree | 23593120 | Detail |
| <0.001 | Malignant neoplasm of breast | Seven SNPs were statistically significant (P ≤ 0.05) with the risk of overall br... | BeFree | 23593120 | Detail |
| 0.132 | Malignant neoplasm of breast | Index SNPs in five loci were replicated, including three associated with ER-/PR-... | BeFree | 23136140 | Detail |
| 0.230 | Malignant neoplasm of breast | Seven SNPs were statistically significant (P ≤ 0.05) with the risk of overall br... | BeFree | 23593120 | Detail |
| 0.138 | Malignant neoplasm of breast | Seven SNPs were statistically significant (P ≤ 0.05) with the risk of overall br... | BeFree | 23593120 | Detail |
| 0.122 | Malignant neoplasm of breast | Seven SNPs were statistically significant (P ≤ 0.05) with the risk of overall br... | BeFree | 23593120 | Detail |
| 0.009 | breast carcinoma | Index SNPs in five loci were replicated, including three associated with ER-/PR-... | BeFree | 23136140 | Detail |
| <0.001 | breast carcinoma | Seven SNPs were statistically significant (P ≤ 0.05) with the risk of overall br... | BeFree | 23593120 | Detail |
| 0.009 | breast carcinoma | Seven SNPs were statistically significant (P ≤ 0.05) with the risk of overall br... | BeFree | 23593120 | Detail |
| 0.138 | Malignant neoplasm of breast | Index SNPs in five loci were replicated, including three associated with ER-/PR-... | BeFree | 23136140 | Detail |
| 0.132 | Malignant neoplasm of breast | Seven SNPs were statistically significant (P ≤ 0.05) with the risk of overall br... | BeFree | 23593120 | Detail |
| 0.120 | Epithelial ovarian cancer | Expression analysis of candidate genes at this locus in ovarian tumors supported... | BeFree | 20852633 | Detail |
| 0.121 | Malignant neoplasm of breast | Genome-wide association studies identify four ER negative-specific breast cancer... | GWASCAT | 23535733 | Detail |
| 0.301 | ovarian neoplasm | Expression analysis of candidate genes at this locus in ovarian tumors supported... | BeFree | 20852633 | Detail |
| 0.123 | ovarian neoplasm | Expression analysis of candidate genes at this locus in ovarian tumors supported... | BeFree | 20852633 | Detail |
| 0.121 | Malignant neoplasm of breast | A locus on 19p13 modifies risk of breast cancer in BRCA1 mutation carriers and i... | GWASCAT | 20852631 | Detail |
| 0.123 | ovarian neoplasm | [Expression analysis of candidate genes at this locus in ovarian tumors supporte... | GAD | 20852633 | Detail |
| 0.120 | Malignant neoplasm of ovary | GWAS meta-analysis and replication identifies three new susceptibility loci for ... | GWASCAT | 23535730 | Detail |
| 0.120 | Epithelial ovarian cancer | Identification of six new susceptibility loci for invasive epithelial ovarian ca... | GWASCAT | 25581431 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| Ten SNPs (rs2075555 in COL1A1, rs12652447 in FBXL17, rs10941679 in 5p12/MRPS30, rs11878583 in ZNF577... | DisGeNET | Detail |
| Ten SNPs (rs2075555 in COL1A1, rs12652447 in FBXL17, rs10941679 in 5p12/MRPS30, rs11878583 in ZNF577... | DisGeNET | Detail |
| We identified six single-nucleotide polymorphisms, including rs2046210 (ESR1), rs12662670 (ESR1), rs... | DisGeNET | Detail |
| We identified six single-nucleotide polymorphisms, including rs2046210 (ESR1), rs12662670 (ESR1), rs... | DisGeNET | Detail |
| We identified six single-nucleotide polymorphisms, including rs2046210 (ESR1), rs12662670 (ESR1), rs... | DisGeNET | Detail |
| Seven SNPs were statistically significant (P ≤ 0.05) with the risk of overall breast cancer in the s... | DisGeNET | Detail |
| Seven SNPs were statistically significant (P ≤ 0.05) with the risk of overall breast cancer in the s... | DisGeNET | Detail |
| Seven SNPs were statistically significant (P ≤ 0.05) with the risk of overall breast cancer in the s... | DisGeNET | Detail |
| Index SNPs in five loci were replicated, including three associated with ER-/PR- breast cancer (TERT... | DisGeNET | Detail |
| Seven SNPs were statistically significant (P ≤ 0.05) with the risk of overall breast cancer in the s... | DisGeNET | Detail |
| Seven SNPs were statistically significant (P ≤ 0.05) with the risk of overall breast cancer in the s... | DisGeNET | Detail |
| Seven SNPs were statistically significant (P ≤ 0.05) with the risk of overall breast cancer in the s... | DisGeNET | Detail |
| Index SNPs in five loci were replicated, including three associated with ER-/PR- breast cancer (TERT... | DisGeNET | Detail |
| Seven SNPs were statistically significant (P ≤ 0.05) with the risk of overall breast cancer in the s... | DisGeNET | Detail |
| Seven SNPs were statistically significant (P ≤ 0.05) with the risk of overall breast cancer in the s... | DisGeNET | Detail |
| Seven SNPs were statistically significant (P ≤ 0.05) with the risk of overall breast cancer in the s... | DisGeNET | Detail |
| Index SNPs in five loci were replicated, including three associated with ER-/PR- breast cancer (TERT... | DisGeNET | Detail |
| Seven SNPs were statistically significant (P ≤ 0.05) with the risk of overall breast cancer in the s... | DisGeNET | Detail |
| Seven SNPs were statistically significant (P ≤ 0.05) with the risk of overall breast cancer in the s... | DisGeNET | Detail |
| Index SNPs in five loci were replicated, including three associated with ER-/PR- breast cancer (TERT... | DisGeNET | Detail |
| Seven SNPs were statistically significant (P ≤ 0.05) with the risk of overall breast cancer in the s... | DisGeNET | Detail |
| Expression analysis of candidate genes at this locus in ovarian tumors supported a role for the BRCA... | DisGeNET | Detail |
| Genome-wide association studies identify four ER negative-specific breast cancer risk loci. | DisGeNET | Detail |
| Expression analysis of candidate genes at this locus in ovarian tumors supported a role for the BRCA... | DisGeNET | Detail |
| Expression analysis of candidate genes at this locus in ovarian tumors supported a role for the BRCA... | DisGeNET | Detail |
| A locus on 19p13 modifies risk of breast cancer in BRCA1 mutation carriers and is associated with ho... | DisGeNET | Detail |
| [Expression analysis of candidate genes at this locus in ovarian tumors supported a role for the BRC... | DisGeNET | Detail |
| GWAS meta-analysis and replication identifies three new susceptibility loci for ovarian cancer. | DisGeNET | Detail |
| Identification of six new susceptibility loci for invasive epithelial ovarian cancer. | 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
- -
- Genome
- hg19
- Position
- chr19:17,389,704-17,389,704
- Variant Type
- snv
- Reference Allele
- G
- Alternative Allele
- A
- Filtering Status (HGVD)
- PASS
- Filtering Status (HGVD)
- LowQual
- # of samples (HGVD)
- 1209
- Mean of sample read depth (HGVD)
- 73.43
- Standard deviation of sample read depth (HGVD)
- 35.41
- Number of reference allele (HGVD)
- 2416
- Number of alternative allele (HGVD)
- 2
- Allele Frequency (HGVD)
- 8.271298593879239E-4
- Gene Symbol (HGVD)
- BABAM1
- 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))
- rs8170
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.0001
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 1
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8468
- East Asian Allele Counts (ExAC)
- 6
- East Asian Heterozygous Counts (ExAC)
- 6
- East Asian Homozygous Counts (ExAC)
- 0
- East Asian Allele Frequency (ExAC)
- 7.085498346717053E-4
- Chromosome Counts in All Race (ExAC)
- 115298
- Allele Counts in All Race (ExAC)
- 18080
- Heterozygous Counts in All Race (ExAC)
- 14918
- Homozygous Counts in All Race (ExAC)
- 1581
- Allele Frequency in All Race (ExAC)
- 0.15681104615864977
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