chr3:14193889:C>T Detail (hg19) (XPC)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr3:14,193,889-14,193,889 |
| hg38 | chr3:14,152,389-14,152,389 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_004628.4:c.2061G>A | NP_004619.3:p.Arg687= |
| Ensemble | ENST00000285021.12:c.2061G>A | ENST00000285021.12:p.Arg687= |
Summary
MGeND
| Clinical significance | |
| Variant entry | |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.042 |
| ToMMo:0.035 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.048 |
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
|
2021-06-16 | criteria provided, multiple submitters, no conflicts | not specified |
germline
|
Detail |
|
Benign
|
2021-12-05 | criteria provided, multiple submitters, no conflicts | Xeroderma pigmentosum, group C |
germline
|
Detail |
|
Benign
|
2024-02-01 | criteria provided, multiple submitters, no conflicts | not provided |
germline
|
Detail |
|
Benign
|
2023-07-07 | criteria provided, single submitter | xeroderma pigmentosum group A |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.005 | breast carcinoma | We evaluated associations between seven single-nucleotide polymorphisms in four ... | BeFree | 21622940 | Detail |
| 0.018 | breast carcinoma | We evaluated associations between seven single-nucleotide polymorphisms in four ... | BeFree | 21622940 | Detail |
| 0.098 | Malignant neoplasm of breast | We evaluated associations between seven single-nucleotide polymorphisms in four ... | BeFree | 21622940 | Detail |
| 0.002 | breast carcinoma | We evaluated associations between seven single-nucleotide polymorphisms in four ... | BeFree | 21622940 | Detail |
| 0.026 | Malignant neoplasm of breast | We evaluated associations between seven single-nucleotide polymorphisms in four ... | BeFree | 21622940 | Detail |
| 0.023 | Malignant neoplasm of breast | We evaluated associations between seven single-nucleotide polymorphisms in four ... | BeFree | 21622940 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_004628.5(XPC):c.2061G>A (p.Arg687=) AND not specified | ClinVar | Detail |
| NM_004628.5(XPC):c.2061G>A (p.Arg687=) AND Xeroderma pigmentosum, group C | ClinVar | Detail |
| NM_004628.5(XPC):c.2061G>A (p.Arg687=) AND not provided | ClinVar | Detail |
| NM_004628.5(XPC):c.2061G>A (p.Arg687=) AND Xeroderma pigmentosum group A | ClinVar | Detail |
| We evaluated associations between seven single-nucleotide polymorphisms in four DNA repair genes (ER... | DisGeNET | Detail |
| We evaluated associations between seven single-nucleotide polymorphisms in four DNA repair genes (ER... | DisGeNET | Detail |
| We evaluated associations between seven single-nucleotide polymorphisms in four DNA repair genes (ER... | DisGeNET | Detail |
| We evaluated associations between seven single-nucleotide polymorphisms in four DNA repair genes (ER... | DisGeNET | Detail |
| We evaluated associations between seven single-nucleotide polymorphisms in four DNA repair genes (ER... | DisGeNET | Detail |
| We evaluated associations between seven single-nucleotide polymorphisms in four DNA repair genes (ER... | 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
- rs2227998 dbSNP
- Genome
- hg19
- Position
- chr3:14,193,889-14,193,889
- Variant Type
- snv
- Reference Allele
- C
- Alternative Allele
- T
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1203
- Mean of sample read depth (HGVD)
- 79.62
- Standard deviation of sample read depth (HGVD)
- 40.37
- Number of reference allele (HGVD)
- 2306
- Number of alternative allele (HGVD)
- 100
- Allele Frequency (HGVD)
- 0.04156275976724855
- Gene Symbol (HGVD)
- XPC
- 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))
- rs2227998
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.0349
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 585
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 7564
- East Asian Allele Counts (ExAC)
- 361
- East Asian Heterozygous Counts (ExAC)
- 355
- East Asian Homozygous Counts (ExAC)
- 3
- East Asian Allele Frequency (ExAC)
- 0.04772607086197779
- Chromosome Counts in All Race (ExAC)
- 109774
- Allele Counts in All Race (ExAC)
- 30013
- Heterozygous Counts in All Race (ExAC)
- 22233
- Homozygous Counts in All Race (ExAC)
- 3890
- Allele Frequency in All Race (ExAC)
- 0.27340718202853137
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