chr5:112164561:G>A Detail (hg19) (APC)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr5:112,164,561-112,164,561 |
| hg38 | chr5:112,828,864-112,828,864 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_000038.5:c.1635G>A | NP_000029.2:p.Ala545= |
| NM_001127510.2:c.1635G>A | NP_001120982.1:p.Ala545= | |
| NM_001127511.2:c.1581G>A | NP_001120983.2:p.Ala527= |
Summary
MGeND
| Clinical significance |
Benign
|
| Variant entry | 3,540 |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.855 |
| ToMMo:0.858 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.823 |
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
|
2020/04/20 | cervical part of oesophagus |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | abdominal part of oesophagus |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | upper third of oesophagus |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | middle third of oesophagus |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | lower third of oesophagus |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | oesophagus, unspecified |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | fundus of stomach |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | body of stomach |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | pyloric antrum |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | stomach, unspecified |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | duodenum |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | jejunum |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | ileum |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | small intestine, unspecified |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | caecum |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | appendix |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | transverse colon |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | descending colon |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | sigmoid colon |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | overlapping lesion of colon |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | colon, unspecified |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | malignant neoplasm of rectosigmoid junction |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | malignant neoplasm of rectum |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | anal canal |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | liver cell carcinoma |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | intrahepatic bile duct carcinoma |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | malignant neoplasm of gallbladder |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | extrahepatic bile duct |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | ampulla of vater |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | head of pancreas |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | body of pancreas |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | tail of pancreas |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | ill-defined sites within the digestive system |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | bronchus or lung, unspecified |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | colon, unspecified |
not provided
|
MGS000040
(TMGS000095) |
Hitoshi Nakagama | National Cancer Center Japan |
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
|
Benign
|
2016-03-16 | criteria provided, multiple submitters, no conflicts | not specified |
germline
unknown
|
Detail |
other
|
no assertion criteria provided | Familial colorectal cancer |
unknown
|
Detail | |
|
Benign
|
2016-03-18 | criteria provided, multiple submitters, no conflicts | Hereditary cancer-predisposing syndrome |
germline
|
Detail |
|
Benign
|
2018-01-13 | criteria provided, single submitter | APC-Associated Polyposis Disorders |
germline
|
Detail |
|
Benign
|
2023-02-19 | reviewed by expert panel | familial adenomatous polyposis 1 |
germline
unknown
|
Detail |
|
Benign
|
no assertion criteria provided | Carcinoma of colon |
unknown
|
Detail | |
|
Benign
|
2023-11-29 | criteria provided, multiple submitters, no conflicts | not provided |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.201 | Malignant neoplasm of ovary | We studied nine single nucleotide polymorphisms (SNPs) located in CTNNB1 (β-cate... | BeFree | 24078348 | Detail |
| 0.002 | ovarian carcinoma | Our study demonstrated significantly increased APC rs11954856 and rs351771 SNP f... | BeFree | 24078348 | Detail |
| 0.280 | Malignant neoplasm of ovary | We studied nine single nucleotide polymorphisms (SNPs) located in CTNNB1 (β-cate... | BeFree | 24078348 | Detail |
| <0.001 | ovarian carcinoma | We studied nine single nucleotide polymorphisms (SNPs) located in CTNNB1 (β-cate... | BeFree | 24078348 | Detail |
| 0.082 | Malignant neoplasm of ovary | Our study demonstrated significantly increased APC rs11954856 and rs351771 SNP f... | BeFree | 24078348 | Detail |
| 0.003 | Malignant neoplasm of ovary | We studied nine single nucleotide polymorphisms (SNPs) located in CTNNB1 (β-cate... | BeFree | 24078348 | Detail |
| 0.002 | ovarian carcinoma | We studied nine single nucleotide polymorphisms (SNPs) located in CTNNB1 (β-cate... | BeFree | 24078348 | Detail |
| 0.082 | ovarian carcinoma | We studied nine single nucleotide polymorphisms (SNPs) located in CTNNB1 (β-cate... | BeFree | 24078348 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_000038.6(APC):c.1635G>A (p.Ala545=) AND not specified | ClinVar | Detail |
| NM_000038.6(APC):c.1635G>A (p.Ala545=) AND Familial colorectal cancer | ClinVar | Detail |
| NM_000038.6(APC):c.1635G>A (p.Ala545=) AND Hereditary cancer-predisposing syndrome | ClinVar | Detail |
| NM_000038.6(APC):c.1635G>A (p.Ala545=) AND APC-Associated Polyposis Disorders | ClinVar | Detail |
| NM_000038.6(APC):c.1635G>A (p.Ala545=) AND Familial adenomatous polyposis 1 | ClinVar | Detail |
| NM_000038.6(APC):c.1635G>A (p.Ala545=) AND Carcinoma of colon | ClinVar | Detail |
| NM_000038.6(APC):c.1635G>A (p.Ala545=) AND not provided | ClinVar | Detail |
| We studied nine single nucleotide polymorphisms (SNPs) located in CTNNB1 (β-catenin) [rs4533622, rs2... | DisGeNET | Detail |
| Our study demonstrated significantly increased APC rs11954856 and rs351771 SNP frequencies in Polish... | DisGeNET | Detail |
| We studied nine single nucleotide polymorphisms (SNPs) located in CTNNB1 (β-catenin) [rs4533622, rs2... | DisGeNET | Detail |
| We studied nine single nucleotide polymorphisms (SNPs) located in CTNNB1 (β-catenin) [rs4533622, rs2... | DisGeNET | Detail |
| Our study demonstrated significantly increased APC rs11954856 and rs351771 SNP frequencies in Polish... | DisGeNET | Detail |
| We studied nine single nucleotide polymorphisms (SNPs) located in CTNNB1 (β-catenin) [rs4533622, rs2... | DisGeNET | Detail |
| We studied nine single nucleotide polymorphisms (SNPs) located in CTNNB1 (β-catenin) [rs4533622, rs2... | DisGeNET | Detail |
| We studied nine single nucleotide polymorphisms (SNPs) located in CTNNB1 (β-catenin) [rs4533622, rs2... | 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
- rs351771 dbSNP
- Genome
- hg19
- Position
- chr5:112,164,561-112,164,561
- Variant Type
- snv
- Reference Allele
- G
- Alternative Allele
- A
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1207
- Mean of sample read depth (HGVD)
- 78.75
- Standard deviation of sample read depth (HGVD)
- 32.98
- Number of reference allele (HGVD)
- 350
- Number of alternative allele (HGVD)
- 2064
- Allele Frequency (HGVD)
- 0.8550124275062138
- Gene Symbol (HGVD)
- APC
- 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))
- rs351771
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.8575
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 14371
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8606
- East Asian Allele Counts (ExAC)
- 7083
- East Asian Heterozygous Counts (ExAC)
- 1263
- East Asian Homozygous Counts (ExAC)
- 2910
- East Asian Allele Frequency (ExAC)
- 0.8230304438763654
- Chromosome Counts in All Race (ExAC)
- 121146
- Allele Counts in All Race (ExAC)
- 78516
- Heterozygous Counts in All Race (ExAC)
- 26680
- Homozygous Counts in All Race (ExAC)
- 25918
- Allele Frequency in All Race (ExAC)
- 0.6481105443019167
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