chr4:54736599:G>C Detail (hg38) (KIT)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr4:55,602,765-55,602,765 View the variant detail on this assembly version. |
| hg38 | chr4:54,736,599-54,736,599 |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_000222.2:c.2586G>C | NP_000213.1:p.Leu862= |
| NM_001093772.1:c.2574G>C | NP_001087241.1:p.Leu858= | |
| Ensemble | ENST00000288135.6:c.2586G>C | ENST00000288135.6:p.Leu862= |
Summary
MGeND
| Clinical significance |
Benign
|
| Variant entry | 1 |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.040 |
| ToMMo:0.047 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.050 |
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
|
Centenarian |
germline
|
MGS000068
(TMGS000140) |
Kenjiro Kosaki | Keio University |
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
|
Benign
|
criteria provided, single submitter | not specified |
germline
|
Detail | |
|
Likely benign
|
2017-04-27 | criteria provided, single submitter | piebaldism |
germline
|
Detail |
|
Benign
Likely benign
|
2024-02-01 | criteria provided, multiple submitters, no conflicts | gastrointestinal stromal tumor |
germline
|
Detail |
|
Likely benign
|
2017-04-27 | criteria provided, single submitter | mastocytosis |
germline
|
Detail |
|
Benign
|
2018-11-08 | criteria provided, single submitter | Hereditary cancer-predisposing syndrome |
germline
|
Detail |
|
Benign
|
2019-03-15 | criteria provided, single submitter | not provided |
germline
|
Detail |
CIViC
| Disease | Drug | EL | ET | ED | CS | VO | TR | Pubmed | Links |
|---|---|---|---|---|---|---|---|---|---|
| acute myeloid leukemia | Selumetinib | B |
Predictive
|
Supports
|
Sensitivity/Response | Common Germline | 1 | 24178622 | Detail |
DisGeNET
[No Data.]
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| Patients with relapsed/refractory AML or 60 years old or more with untreated AML were enrolled on a ... | CIViC Evidence | Detail |
| NM_000222.3(KIT):c.2586G>C (p.Leu862=) AND not specified | ClinVar | Detail |
| NM_000222.3(KIT):c.2586G>C (p.Leu862=) AND Piebaldism | ClinVar | Detail |
| NM_000222.3(KIT):c.2586G>C (p.Leu862=) AND Gastrointestinal stromal tumor | ClinVar | Detail |
| NM_000222.3(KIT):c.2586G>C (p.Leu862=) AND Mastocytosis | ClinVar | Detail |
| NM_000222.3(KIT):c.2586G>C (p.Leu862=) AND Hereditary cancer-predisposing syndrome | ClinVar | Detail |
| NM_000222.3(KIT):c.2586G>C (p.Leu862=) 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
- rs3733542 dbSNP
- Genome
- hg38
- Position
- chr4:54,736,599-54,736,599
- Variant Type
- snv
- Reference Allele
- G
- Alternative Allele
- C
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1210
- Mean of sample read depth (HGVD)
- 123.99
- Standard deviation of sample read depth (HGVD)
- 55.38
- Number of reference allele (HGVD)
- 2324
- Number of alternative allele (HGVD)
- 96
- Allele Frequency (HGVD)
- 0.03966942148760331
- Gene Symbol (HGVD)
- KIT
- 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))
- rs3733542
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.0473
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 792
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8644
- East Asian Allele Counts (ExAC)
- 428
- East Asian Heterozygous Counts (ExAC)
- 414
- East Asian Homozygous Counts (ExAC)
- 7
- East Asian Allele Frequency (ExAC)
- 0.04951411383618695
- Chromosome Counts in All Race (ExAC)
- 121360
- Allele Counts in All Race (ExAC)
- 14061
- Heterozygous Counts in All Race (ExAC)
- 11801
- Homozygous Counts in All Race (ExAC)
- 1130
- Allele Frequency in All Race (ExAC)
- 0.1158618984838497
- Variant (CIViC) (CIViC Variant)
- RS3733542
- Transcript 1 (CIViC Variant)
- ENST00000288135.5
- Variant URL (CIViC Variant)
- https://civic.genome.wustl.edu/links/variants/482
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