chr20:46014472:G>A Detail (hg38) (MMP9, SLC12A5-AS1)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr20:44,643,111-44,643,111 View the variant detail on this assembly version. |
| hg38 | chr20:46,014,472-46,014,472 |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_004994.2:c.2003G>A | NP_004985.2:p.Arg668Gln |
| Ensemble | ENST00000372330.3:c.2003G>A | ENST00000372330.3:p.Arg668Gln |
Summary
MGeND
| Clinical significance | |
| Variant entry | |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.185 |
| ToMMo:0.190 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.147 |
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 |
|---|---|---|---|---|---|
|
Benign
|
2021-09-05 | criteria provided, multiple submitters, no conflicts | Metaphyseal anadysplasia 2 |
germline
|
Detail |
|
Benign
|
2017-08-10 | criteria provided, single submitter | not specified |
germline
|
Detail |
|
Benign
|
2024-01-31 | criteria provided, multiple submitters, no conflicts | not provided |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.011 | coronary artery disease | We explored the association of MMP2 (C-735T, rs2285053), MMP7 (A-181G, rs1156881... | BeFree | 22664146 | Detail |
| 0.030 | coronary artery disease | These findings suggest that MMP-9 R279Q, P574R and R668Q may have combined effec... | BeFree | 19283512 | Detail |
| 0.001 | gallbladder carcinoma | Multidimensional reduction analysis revealed LXR-β (rs3546355 G > A, rs269512... | BeFree | 24863943 | Detail |
| <0.001 | gallbladder carcinoma | Multidimensional reduction analysis revealed LXR-β (rs3546355 G > A, rs269512... | BeFree | 24863943 | Detail |
| <0.001 | Malignant neoplasm of gallbladder | Multidimensional reduction analysis revealed LXR-β (rs3546355 G > A, rs269512... | BeFree | 24863943 | Detail |
| 0.163 | squamous cell carcinoma | This study provides evidence for the contribution of the MMP9 Arg668Gln to SCC d... | BeFree | 19064570 | Detail |
| 0.001 | Malignant neoplasm of gallbladder | Multidimensional reduction analysis revealed LXR-β (rs3546355 G > A, rs269512... | BeFree | 24863943 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_004994.3(MMP9):c.2003G>A (p.Arg668Gln) AND Metaphyseal anadysplasia 2 | ClinVar | Detail |
| NM_004994.3(MMP9):c.2003G>A (p.Arg668Gln) AND not specified | ClinVar | Detail |
| NM_004994.3(MMP9):c.2003G>A (p.Arg668Gln) AND not provided | ClinVar | Detail |
| We explored the association of MMP2 (C-735T, rs2285053), MMP7 (A-181G, rs11568818) and MMP9 (R279Q, ... | DisGeNET | Detail |
| These findings suggest that MMP-9 R279Q, P574R and R668Q may have combined effect in the occurrence ... | DisGeNET | Detail |
| Multidimensional reduction analysis revealed LXR-β (rs3546355 G > A, rs2695121 T > C), MMP-2 (... | DisGeNET | Detail |
| Multidimensional reduction analysis revealed LXR-β (rs3546355 G > A, rs2695121 T > C), MMP-2 (... | DisGeNET | Detail |
| Multidimensional reduction analysis revealed LXR-β (rs3546355 G > A, rs2695121 T > C), MMP-2 (... | DisGeNET | Detail |
| This study provides evidence for the contribution of the MMP9 Arg668Gln to SCC development. | DisGeNET | Detail |
| Multidimensional reduction analysis revealed LXR-β (rs3546355 G > A, rs2695121 T > C), MMP-2 (... | 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
- rs17577 dbSNP
- Genome
- hg38
- Position
- chr20:46,014,472-46,014,472
- Variant Type
- snv
- Reference Allele
- G
- Alternative Allele
- A
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1204
- Mean of sample read depth (HGVD)
- 114.98
- Standard deviation of sample read depth (HGVD)
- 61.37
- Number of reference allele (HGVD)
- 1962
- Number of alternative allele (HGVD)
- 446
- Allele Frequency (HGVD)
- 0.1852159468438538
- Gene Symbol (HGVD)
- MMP9
- 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))
- rs17577
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.1904
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 3191
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 590
- East Asian Allele Counts (ExAC)
- 87
- East Asian Heterozygous Counts (ExAC)
- 77
- East Asian Homozygous Counts (ExAC)
- 5
- East Asian Allele Frequency (ExAC)
- 0.14745762711864407
- Chromosome Counts in All Race (ExAC)
- 19836
- Allele Counts in All Race (ExAC)
- 4281
- Heterozygous Counts in All Race (ExAC)
- 3247
- Homozygous Counts in All Race (ExAC)
- 517
- Allele Frequency in All Race (ExAC)
- 0.21581972171808833
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