chr5:147828020:A>G Detail (hg38) (SPINK1)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr5:147,207,583-147,207,583 View the variant detail on this assembly version. |
| hg38 | chr5:147,828,020-147,828,020 |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_003122.4:c.194+2T>C | |
| Ensemble | ENST00000296695.10:c.194+2T>C | |
| ENST00000510027.2:c.196T>C | ENST00000510027.2:p.Ter66Argext*? |
Summary
MGeND
| Clinical significance |
Pathogenic
|
| Variant entry | 4 |
| 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:0.004 |
Prediction
ClinVar
| Clinical Significance | Conflicting classifications of pathogenicity |
| Review star |  |
| Show details | |
Disease area statistics
MGeND
| Clinical significance | Last evaluated | Condition | Origin | Submission ID | Submitter | Institute | Citation | Comment | Image |
|---|---|---|---|---|---|---|---|---|---|
|
Pathogenic
|
2021/07/11 | hereditary pancreatitis |
germline
|
MGS000029
(TMGS000133) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Pathogenic
|
2021/07/11 | other chronic pancreatitis |
germline
|
MGS000029
(TMGS000133) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Pathogenic
|
other |
germline
|
MGS000001
(TMGS000137) |
Kenjiro Kosaki | Keio University |
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
Conflicting interpretations of pathogenicity
|
2024-01-26 | criteria provided, conflicting interpretations | Hereditary pancreatitis |
germline
|
Detail |
|
Pathogenic
|
2017-01-01 | criteria provided, single submitter |
unknown
|
Detail | |
|
Pathogenic
|
2018-10-31 | criteria provided, single submitter | Hereditary pancreatitis,Tropical pancreatitis |
unknown
|
Detail |
|
Pathogenic
|
2018-10-31 | criteria provided, single submitter | Hereditary pancreatitis,Tropical pancreatitis |
unknown
|
Detail |
|
Pathogenic
|
no assertion criteria provided | diabetes mellitus |
unknown
|
Detail | |
Pathogenic
Likely pathogenic
|
2024-04-01 | criteria provided, multiple submitters, no conflicts | not provided |
germline
|
Detail |
|
Pathogenic
|
2023-08-24 | criteria provided, single submitter | SPINK1-related disorder |
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.194+2T>C AND Hereditary pancreatitis | ClinVar | Detail |
| NM_001379610.1(SPINK1):c.194+2T>C AND Chronic pancreatitis | ClinVar | Detail |
| NM_001379610.1(SPINK1):c.194+2T>C AND multiple conditions | ClinVar | Detail |
| NM_001379610.1(SPINK1):c.194+2T>C AND multiple conditions | ClinVar | Detail |
| NM_001379610.1(SPINK1):c.194+2T>C AND Diabetes mellitus | ClinVar | Detail |
| NM_001379610.1(SPINK1):c.194+2T>C AND not provided | ClinVar | Detail |
| NM_001379610.1(SPINK1):c.194+2T>C AND SPINK1-related disorder | 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
- rs148954387 dbSNP
- Genome
- hg38
- Position
- chr5:147,828,020-147,828,020
- Variant Type
- snv
- Reference Allele
- A
- Alternative Allele
- G
- Filtering Status (HGVD)
- PASS
- Filtering Status (HGVD)
- LowQual
- # of samples (HGVD)
- 1210
- Mean of sample read depth (HGVD)
- 53.85
- Standard deviation of sample read depth (HGVD)
- 25.27
- Number of reference allele (HGVD)
- 2417
- Number of alternative allele (HGVD)
- 3
- Allele Frequency (HGVD)
- 0.0012396694214876034
- 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))
- rs148954387
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.001
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 17
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 7360
- East Asian Allele Counts (ExAC)
- 26
- East Asian Heterozygous Counts (ExAC)
- 26
- East Asian Homozygous Counts (ExAC)
- 0
- East Asian Allele Frequency (ExAC)
- 0.003532608695652174
- Chromosome Counts in All Race (ExAC)
- 97938
- Allele Counts in All Race (ExAC)
- 35
- Heterozygous Counts in All Race (ExAC)
- 35
- Homozygous Counts in All Race (ExAC)
- 0
- Allele Frequency in All Race (ExAC)
- 3.5736894770160713E-4
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