chr2:136115514:G>A Detail (hg38) (CXCR4)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr2:136,873,084-136,873,084 View the variant detail on this assembly version. |
| hg38 | chr2:136,115,514-136,115,514 |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_003467.2:c.414C>T | NP_003458.1:p.Ile138= |
| NM_001008540.1:c.426C>T | NP_001008540.1:p.Ile142= | |
| Ensemble | ENST00000241393.4:c.414C>T | ENST00000241393.4:p.Ile138= |
Summary
MGeND
| Clinical significance |
Benign
|
| Variant entry | 1 |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.088 |
| ToMMo:0.071 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.120 |
Prediction
ClinVar
| Clinical Significance |
Benign
|
| Review star |  |
| Show details | |
Disease area statistics
MGeND
| Clinical significance | Last evaluated | Condition | Origin | Submission ID | Submitter | Institute | Citation | Comment | Image |
|---|---|---|---|---|---|---|---|---|---|
|
Benign
|
Centenarian |
germline
|
MGS000068
(TMGS000140) |
Kenjiro Kosaki | Keio University |
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
|
Benign
|
criteria provided, single submitter | not specified |
germline
|
Detail | |
|
Benign
|
2024-02-01 | criteria provided, single submitter | Warts, hypogammaglobulinemia, infections, and myelokathexis |
germline
|
Detail |
|
Benign
|
2020-10-06 | criteria provided, single submitter | not provided |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.029 | Malignant neoplasm of breast | Similarly, the SNP barcode of rs12812942-rs2228014-rs3025039 (CD4-CXCR4-VEGF) an... | BeFree | 19196101 | Detail |
| 0.006 | Malignant neoplasm of breast | Similarly, the SNP barcode of rs12812942-rs2228014-rs3025039 (CD4-CXCR4-VEGF) an... | BeFree | 19196101 | Detail |
| 0.004 | breast carcinoma | Similarly, the SNP barcode of rs12812942-rs2228014-rs3025039 (CD4-CXCR4-VEGF) an... | BeFree | 19196101 | Detail |
| 0.026 | breast carcinoma | Similarly, the SNP barcode of rs12812942-rs2228014-rs3025039 (CD4-CXCR4-VEGF) an... | BeFree | 19196101 | Detail |
| 0.065 | breast carcinoma | Similarly, the SNP barcode of rs12812942-rs2228014-rs3025039 (CD4-CXCR4-VEGF) an... | BeFree | 19196101 | Detail |
| 0.105 | Malignant neoplasm of breast | Similarly, the SNP barcode of rs12812942-rs2228014-rs3025039 (CD4-CXCR4-VEGF) an... | BeFree | 19196101 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_003467.3(CXCR4):c.414C>T (p.Ile138=) AND not specified | ClinVar | Detail |
| NM_003467.3(CXCR4):c.414C>T (p.Ile138=) AND Warts, hypogammaglobulinemia, infections, and myelokathe... | ClinVar | Detail |
| NM_003467.3(CXCR4):c.414C>T (p.Ile138=) AND not provided | ClinVar | Detail |
| Similarly, the SNP barcode of rs12812942-rs2228014-rs3025039 (CD4-CXCR4-VEGF) and rs12812942-rs31366... | DisGeNET | Detail |
| Similarly, the SNP barcode of rs12812942-rs2228014-rs3025039 (CD4-CXCR4-VEGF) and rs12812942-rs31366... | DisGeNET | Detail |
| Similarly, the SNP barcode of rs12812942-rs2228014-rs3025039 (CD4-CXCR4-VEGF) and rs12812942-rs31366... | DisGeNET | Detail |
| Similarly, the SNP barcode of rs12812942-rs2228014-rs3025039 (CD4-CXCR4-VEGF) and rs12812942-rs31366... | DisGeNET | Detail |
| Similarly, the SNP barcode of rs12812942-rs2228014-rs3025039 (CD4-CXCR4-VEGF) and rs12812942-rs31366... | DisGeNET | Detail |
| Similarly, the SNP barcode of rs12812942-rs2228014-rs3025039 (CD4-CXCR4-VEGF) and rs12812942-rs31366... | 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
- rs2228014 dbSNP
- Genome
- hg38
- Position
- chr2:136,115,514-136,115,514
- Variant Type
- snv
- Reference Allele
- G
- Alternative Allele
- A
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1210
- Mean of sample read depth (HGVD)
- 156.55
- Standard deviation of sample read depth (HGVD)
- 73.87
- Number of reference allele (HGVD)
- 2206
- Number of alternative allele (HGVD)
- 214
- Allele Frequency (HGVD)
- 0.0884297520661157
- Gene Symbol (HGVD)
- CXCR4
- 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))
- rs2228014
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.0707
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 1185
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8650
- East Asian Allele Counts (ExAC)
- 1042
- East Asian Heterozygous Counts (ExAC)
- 914
- East Asian Homozygous Counts (ExAC)
- 64
- East Asian Allele Frequency (ExAC)
- 0.12046242774566474
- Chromosome Counts in All Race (ExAC)
- 121396
- Allele Counts in All Race (ExAC)
- 5583
- Heterozygous Counts in All Race (ExAC)
- 5173
- Homozygous Counts in All Race (ExAC)
- 205
- Allele Frequency in All Race (ExAC)
- 0.04598998319549244
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