chr1:65310489:T>C Detail (hg19) (JAK1)

Information

Genome

Assembly Position
hg19 chr1:65,310,489-65,310,489
hg38 chr1:64,844,806-64,844,806 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_001320923.1:c.2199A>G NP_001307852.1:p.Pro733=
NM_001321852.1:c.2199A>G NP_001308781.1:p.Pro733=
NM_001321853.1:c.2199A>G NP_001308782.1:p.Pro733=
Summary

MGeND

Clinical significance not provided
Variant entry 4,564
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.280
ToMMo:0.275
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.314

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 147795 OMIM
HGNC 6190 HGNC
Ensembl ENSG00000162434 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv1805539 TogoVar
COSMIC COSM3751351 COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
not provided colon, unspecified not provided MGS000040
(TMGS000095) 		Hitoshi Nakagama National Cancer Center Japan
not provided cervical part of oesophagus not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
not provided abdominal part of oesophagus not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
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 anal canal 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 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
not provided cervical part of oesophagus not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
not provided abdominal part of oesophagus not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
not provided upper third of oesophagus not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
not provided middle third of oesophagus not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
not provided lower third of oesophagus not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
not provided oesophagus, unspecified not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
not provided fundus of stomach not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
not provided body of stomach not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
not provided pyloric antrum not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
not provided stomach, unspecified not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
not provided duodenum not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
not provided jejunum not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
not provided ileum not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
not provided small intestine, unspecified not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
not provided caecum not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
not provided appendix not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
not provided transverse colon not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
not provided descending colon not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
not provided colon, unspecified not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
not provided malignant neoplasm of rectosigmoid junction not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
not provided malignant neoplasm of rectum not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
not provided anal canal not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
not provided liver cell carcinoma not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
not provided intrahepatic bile duct carcinoma not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
not provided malignant neoplasm of gallbladder not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
not provided extrahepatic bile duct not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
not provided ampulla of vater not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
not provided head of pancreas not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
not provided body of pancreas not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
not provided tail of pancreas not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
not provided ill-defined sites within the digestive system not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
not provided bronchus or lung, unspecified not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2024-02-01 criteria provided, single submitter not provided germline Detail
Benign 2023-11-12 criteria provided, single submitter not specified germline Detail
CIViC
[No Data.]
DisGeNET
[No Data.]
Annotation

Annotations

DescrptionSourceLinks
NM_002227.4(JAK1):c.2199A>G (p.Pro733=) AND not provided ClinVar Detail
NM_002227.4(JAK1):c.2199A>G (p.Pro733=) 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
rs2230588 dbSNP
Genome
hg19
Position
chr1:65,310,489-65,310,489
Variant Type
snv
Reference Allele
T
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1206
Mean of sample read depth (HGVD)
51.88
Standard deviation of sample read depth (HGVD)
22.78
Number of reference allele (HGVD)
1736
Number of alternative allele (HGVD)
676
Allele Frequency (HGVD)
0.2802653399668325
Gene Symbol (HGVD)
JAK1
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))
rs2230588
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.2748
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
4606
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8612
East Asian Allele Counts (ExAC)
2701
East Asian Heterozygous Counts (ExAC)
1787
East Asian Homozygous Counts (ExAC)
457
East Asian Allele Frequency (ExAC)
0.31363214119832794
Chromosome Counts in All Race (ExAC)
120704
Allele Counts in All Race (ExAC)
35431
Heterozygous Counts in All Race (ExAC)
23437
Homozygous Counts in All Race (ExAC)
5997
Allele Frequency in All Race (ExAC)
0.2935362539766702
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