chr4:55602765:G>C Detail (hg19) (KIT)

Information

Genome

Assembly Position
hg19 chr4:55,602,765-55,602,765
hg38 chr4:54,736,599-54,736,599 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_001093772.1:c.2574G>C NP_001087241.1:p.Leu858=
NM_000222.2:c.2586G>C NP_000213.1:p.Leu862=
Ensemble ENST00000412167.7:c.2574G>C ENST00000412167.7:p.Leu858=
Summary

MGeND

Clinical significance Benign not provided
Variant entry 508
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
Links
Type Database ID Link
Gene MIM 164920 OMIM
HGNC 6342 HGNC
Ensembl ENSG00000157404 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv17039575 TogoVar
COSMIC COSM1325 COSMIC
MONDO
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
not provided upper third of oesophagus not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
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 ileum 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 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 intrahepatic bile duct carcinoma 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 ampulla of vater 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 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

DescrptionSourceLinks
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
hg19
Position
chr4:55,602,765-55,602,765
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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