chr3:10106532:C>T Detail (hg19) (FANCD2, LOC107303338)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr3:10,106,532-10,106,532 |
| hg38 | chr3:10,064,848-10,064,848 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_001319984.1:c.2141C>T | NP_001306913.1:p.Pro714Leu |
| NM_033084.4:c.2141C>T | NP_149075.2:p.Pro714Leu | |
| Ensemble | ENST00000419585.5:c.2141C>T | ENST00000419585.5:p.Pro714Leu |
Summary
MGeND
| Clinical significance |
Benign
|
| Variant entry | 578 |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.033 |
| ToMMo:0.048 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.059 |
Prediction
ClinVar
| Clinical Significance |
Benign
Likely 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 | upper third of oesophagus |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | middle third of oesophagus |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | lower third of oesophagus |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | oesophagus, unspecified |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | fundus of stomach |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | body of stomach |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | pyloric antrum |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | stomach, unspecified |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | duodenum |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | jejunum |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | ileum |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | caecum |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | appendix |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | ascending colon |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | transverse colon |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | descending colon |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | sigmoid colon |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | colon, unspecified |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | malignant neoplasm of rectosigmoid junction |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | malignant neoplasm of rectum |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | liver cell carcinoma |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | intrahepatic bile duct carcinoma |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | malignant neoplasm of gallbladder |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | extrahepatic bile duct |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | head of pancreas |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | body of pancreas |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | tail of pancreas |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | ill-defined sites within the digestive system |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | bronchus or lung, unspecified |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan |
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
|
Benign
Likely benign
|
2021-12-03 | criteria provided, multiple submitters, no conflicts | not specified |
germline
|
Detail |
|
Benign
|
2024-02-01 | criteria provided, multiple submitters, no conflicts | Fanconi anemia |
germline
|
Detail |
|
Benign
|
2019-05-28 | criteria provided, single submitter | Fanconi anemia complementation group A |
unknown
|
Detail |
|
Benign
|
2023-07-07 | criteria provided, multiple submitters, no conflicts | Fanconi anemia complementation group D2 |
germline
|
Detail |
|
Benign
|
2019-03-01 | criteria provided, single submitter | not provided |
germline
|
Detail |
|
Benign
|
2022-04-19 | criteria provided, single submitter | hereditary breast ovarian cancer syndrome |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
[No Data.]
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_001018115.3(FANCD2):c.2141C>T (p.Pro714Leu) AND not specified | ClinVar | Detail |
| NM_001018115.3(FANCD2):c.2141C>T (p.Pro714Leu) AND Fanconi anemia | ClinVar | Detail |
| NM_001018115.3(FANCD2):c.2141C>T (p.Pro714Leu) AND Fanconi anemia complementation group A | ClinVar | Detail |
| NM_001018115.3(FANCD2):c.2141C>T (p.Pro714Leu) AND Fanconi anemia complementation group D2 | ClinVar | Detail |
| NM_001018115.3(FANCD2):c.2141C>T (p.Pro714Leu) AND not provided | ClinVar | Detail |
| NM_001018115.3(FANCD2):c.2141C>T (p.Pro714Leu) AND Hereditary breast ovarian cancer syndrome | ClinVar | 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
- rs3864017 dbSNP
- Genome
- hg19
- Position
- chr3:10,106,532-10,106,532
- Variant Type
- snv
- Reference Allele
- C
- Alternative Allele
- T
- Filtering Status (HGVD)
- PASS
- Filtering Status (HGVD)
- VQSRTrancheSNP99.00to99.90
- Filtering Status (HGVD)
- LowQual
- # of samples (HGVD)
- 837
- Mean of sample read depth (HGVD)
- 16.13
- Standard deviation of sample read depth (HGVD)
- 46.78
- Number of reference allele (HGVD)
- 1618
- Number of alternative allele (HGVD)
- 56
- Allele Frequency (HGVD)
- 0.03345280764635603
- Gene Symbol (HGVD)
- FANCD2
- ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- VQSRTrancheSNP99.80to99.90
- Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- rs3864017
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.0483
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 809
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8592
- East Asian Allele Counts (ExAC)
- 505
- East Asian Heterozygous Counts (ExAC)
- 497
- East Asian Homozygous Counts (ExAC)
- 4
- East Asian Allele Frequency (ExAC)
- 0.0587756052141527
- Chromosome Counts in All Race (ExAC)
- 120684
- Allele Counts in All Race (ExAC)
- 18644
- Heterozygous Counts in All Race (ExAC)
- 16668
- Homozygous Counts in All Race (ExAC)
- 988
- Allele Frequency in All Race (ExAC)
- 0.1544860959199231
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