chr16:3640853:G>A Detail (hg19) (SLX4)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr16:3,640,853-3,640,853 |
| hg38 | chr16:3,590,852-3,590,852 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_032444.2:c.2786C>T | NP_115820.2:p.Pro929Leu |
| Ensemble | ENST00000294008.4:c.2786C>T | ENST00000294008.4:p.Pro929Leu |
Summary
MGeND
| Clinical significance |
not provided
|
| Variant entry | 228 |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.021 |
| ToMMo:0.020 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.028 |
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 |
|---|---|---|---|---|---|---|---|---|---|
|
not provided
|
middle third of oesophagus |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
lower third of oesophagus |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
oesophagus, unspecified |
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
|
pyloric antrum |
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
|
duodenum |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
jejunum |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
small intestine, unspecified |
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
|
appendix |
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
|
transverse 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
|
liver cell carcinoma |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
intrahepatic bile duct carcinoma |
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
|
tail 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
|
2024-01-15 | criteria provided, single submitter | Fanconi anemia |
germline
|
Detail |
|
Benign
|
2018-08-03 | criteria provided, single submitter | not specified |
germline
|
Detail |
|
Benign
|
2018-01-13 | criteria provided, single submitter | Fanconi anemia complementation group P |
germline
|
Detail |
Likely benign
|
no assertion criteria provided | not provided |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
[No Data.]
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_032444.4(SLX4):c.2786C>T (p.Pro929Leu) AND Fanconi anemia | ClinVar | Detail |
| NM_032444.4(SLX4):c.2786C>T (p.Pro929Leu) AND not specified | ClinVar | Detail |
| NM_032444.4(SLX4):c.2786C>T (p.Pro929Leu) AND Fanconi anemia complementation group P | ClinVar | Detail |
| NM_032444.4(SLX4):c.2786C>T (p.Pro929Leu) 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
- rs117707719 dbSNP
- Genome
- hg19
- Position
- chr16:3,640,853-3,640,853
- Variant Type
- snv
- Reference Allele
- G
- Alternative Allele
- A
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1210
- Mean of sample read depth (HGVD)
- 137.04
- Standard deviation of sample read depth (HGVD)
- 66.88
- Number of reference allele (HGVD)
- 2369
- Number of alternative allele (HGVD)
- 51
- Allele Frequency (HGVD)
- 0.021074380165289255
- 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))
- rs117707719
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.0197
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 331
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8654
- East Asian Allele Counts (ExAC)
- 245
- East Asian Heterozygous Counts (ExAC)
- 241
- East Asian Homozygous Counts (ExAC)
- 2
- East Asian Allele Frequency (ExAC)
- 0.028310607811416685
- Chromosome Counts in All Race (ExAC)
- 121274
- Allele Counts in All Race (ExAC)
- 245
- Heterozygous Counts in All Race (ExAC)
- 241
- Homozygous Counts in All Race (ExAC)
- 2
- Allele Frequency in All Race (ExAC)
- 0.002020218678364695
Genome browser