chr16:3641011:G>A Detail (hg19) (SLX4)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr16:3,641,011-3,641,011 |
| hg38 | chr16:3,591,010-3,591,010 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_032444.2:c.2628C>T | NP_115820.2:p.Asp876= |
| Ensemble | ENST00000294008.4:c.2628C>T | ENST00000294008.4:p.Asp876= |
Summary
MGeND
| Clinical significance |
not provided
|
| Variant entry | 10 |
| 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 |
Benign
Likely benign
|
| Review star |  |
| Show details | |
Disease area statistics
MGeND
| Clinical significance | Last evaluated | Condition | Origin | Submission ID | Submitter | Institute | Citation | Comment | Image |
|---|---|---|---|---|---|---|---|---|---|
|
not provided
|
middle third of oesophagus |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
fundus of stomach |
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
|
stomach, unspecified |
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
|
head 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
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
|
Benign
|
2024-01-17 | criteria provided, single submitter | Fanconi anemia |
germline
|
Detail |
|
Benign
Likely benign
|
2023-07-07 | criteria provided, multiple submitters, no conflicts | Fanconi anemia complementation group P |
germline
|
Detail |
|
Likely benign
|
2012-08-31 | no assertion criteria provided | not specified |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
[No Data.]
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_032444.4(SLX4):c.2628C>T (p.Asp876=) AND Fanconi anemia | ClinVar | Detail |
| NM_032444.4(SLX4):c.2628C>T (p.Asp876=) AND Fanconi anemia complementation group P | ClinVar | Detail |
| NM_032444.4(SLX4):c.2628C>T (p.Asp876=) AND not specified | 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
- rs201279467 dbSNP
- Genome
- hg19
- Position
- chr16:3,641,011-3,641,011
- Variant Type
- snv
- Reference Allele
- G
- Alternative Allele
- A
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1210
- Mean of sample read depth (HGVD)
- 185.75
- Standard deviation of sample read depth (HGVD)
- 85.11
- Number of reference allele (HGVD)
- 2419
- Number of alternative allele (HGVD)
- 1
- Allele Frequency (HGVD)
- 4.1322314049586776E-4
- Gene Symbol (HGVD)
- SLX4
- 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))
- rs201279467
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.0008
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 14
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8652
- East Asian Allele Counts (ExAC)
- 38
- East Asian Heterozygous Counts (ExAC)
- 38
- East Asian Homozygous Counts (ExAC)
- 0
- East Asian Allele Frequency (ExAC)
- 0.00439204808136847
- Chromosome Counts in All Race (ExAC)
- 121396
- Allele Counts in All Race (ExAC)
- 40
- Heterozygous Counts in All Race (ExAC)
- 40
- Homozygous Counts in All Race (ExAC)
- 0
- Allele Frequency in All Race (ExAC)
- 3.2950014827506674E-4
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