chr3:10116221:C>T Detail (hg19) (FANCD2, LOC107303338)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr3:10,116,221-10,116,221 |
| hg38 | chr3:10,074,537-10,074,537 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_033084.4:c.2723C>T | NP_149075.2:p.Thr908Ile |
| NM_001319984.1:c.2723C>T | NP_001306913.1:p.Thr908Ile | |
| Ensemble | ENST00000287647.7:c.2723C>T | ENST00000287647.7:p.Thr908Ile |
Summary
MGeND
| Clinical significance |
Uncertain significance
not provided
|
| Variant entry | 72 |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.005 |
| ToMMo:0.005 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.009 |
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 |
|---|---|---|---|---|---|---|---|---|---|
|
Uncertain significance
|
Pancreas |
germline
|
MGS000038
(TMGS000091) |
Manabu Muto Ichiro Kinoshita |
Kyoto University Department of Medical Oncology Faculty of Medicine and Graduate School of Medicine Hokkaido University |
||||
|
Uncertain significance
|
NSCLC |
germline
|
MGS000038
(TMGS000091) |
Manabu Muto Ichiro Kinoshita |
Kyoto University Department of Medical Oncology Faculty of Medicine and Graduate School of Medicine Hokkaido University |
||||
|
not provided
|
upper third of oesophagus |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
body of stomach |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
pyloric antrum |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
caecum |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
ascending colon |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
descending colon |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
sigmoid colon |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
colon, unspecified |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
malignant neoplasm of rectosigmoid junction |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
malignant neoplasm of rectum |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
malignant neoplasm of gallbladder |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
extrahepatic bile duct |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
head of pancreas |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
body of pancreas |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
ill-defined sites within the digestive system |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
bronchus or lung, unspecified |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan |
ClinVar
CIViC
[No Data.]
DisGeNET
[No Data.]
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_001018115.3(FANCD2):c.2723C>T (p.Thr908Ile) AND Fanconi anemia | ClinVar | Detail |
| NM_001018115.3(FANCD2):c.2723C>T (p.Thr908Ile) AND not provided | 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
- rs188375397 dbSNP
- Genome
- hg19
- Position
- chr3:10,116,221-10,116,221
- Variant Type
- snv
- Reference Allele
- C
- Alternative Allele
- T
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1210
- Mean of sample read depth (HGVD)
- 80.69
- Standard deviation of sample read depth (HGVD)
- 35.83
- Number of reference allele (HGVD)
- 2408
- Number of alternative allele (HGVD)
- 12
- Allele Frequency (HGVD)
- 0.0049586776859504135
- Gene Symbol (HGVD)
- FANCD2
- 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))
- rs188375397
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.0052
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 87
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8630
- East Asian Allele Counts (ExAC)
- 81
- East Asian Heterozygous Counts (ExAC)
- 77
- East Asian Homozygous Counts (ExAC)
- 2
- East Asian Allele Frequency (ExAC)
- 0.009385863267670916
- Chromosome Counts in All Race (ExAC)
- 120824
- Allele Counts in All Race (ExAC)
- 97
- Heterozygous Counts in All Race (ExAC)
- 93
- Homozygous Counts in All Race (ExAC)
- 2
- Allele Frequency in All Race (ExAC)
- 8.028206316625836E-4
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