chr5:147204265:G>A Detail (hg19) (SPINK1)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr5:147,204,265-147,204,265 |
| hg38 | chr5:147,824,702-147,824,702 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_003122.4:c.199C>T | NP_003113.2:p.Arg67Cys |
| Ensemble | ENST00000296695.10:c.199C>T | ENST00000296695.10:p.Arg67Cys |
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 |
Uncertain significance
|
| Review star |  |
| Show details | |
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
|
Uncertain significance
|
2023-04-07 | criteria provided, multiple submitters, no conflicts | Hereditary pancreatitis |
germline
unknown
|
Detail |
|
Uncertain significance
|
2023-05-12 | criteria provided, single submitter | not specified |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.245 | Hereditary pancreatitis | NA | CLINVAR | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_001379610.1(SPINK1):c.199C>T (p.Arg67Cys) AND Hereditary pancreatitis | ClinVar | Detail |
| NM_001379610.1(SPINK1):c.199C>T (p.Arg67Cys) AND not specified | ClinVar | 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
- rs515726208 dbSNP
- Genome
- hg19
- Position
- chr5:147,204,265-147,204,265
- 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)
- 55.40
- Standard deviation of sample read depth (HGVD)
- 26.73
- Number of reference allele (HGVD)
- 2416
- Number of alternative allele (HGVD)
- 2
- Allele Frequency (HGVD)
- 8.271298593879239E-4
- Gene Symbol (HGVD)
- SPINK1
- 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))
- rs515726208
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.0002
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 4
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8442
- East Asian Allele Counts (ExAC)
- 0
- East Asian Heterozygous Counts (ExAC)
- 0
- East Asian Homozygous Counts (ExAC)
- 0
- East Asian Allele Frequency (ExAC)
- 0.0
- Chromosome Counts in All Race (ExAC)
- 119552
- Allele Counts in All Race (ExAC)
- 3
- Heterozygous Counts in All Race (ExAC)
- 3
- Homozygous Counts in All Race (ExAC)
- 0
- Allele Frequency in All Race (ExAC)
- 2.5093683083511777E-5
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