chr2:100974842:A>G Detail (hg38) (NPAS2)

Information

Genome

Assembly Position
hg19 chr2:101,591,304-101,591,304 View the variant detail on this assembly version.
hg38 chr2:100,974,842-100,974,842

HGVS

Type Transcript Protein
RefSeq NM_002518.3:c.1180A>G NP_002509.2:p.Thr394Ala
Ensemble ENST00000335681.10:c.1180A>G ENST00000335681.10:p.Thr394Ala
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.823
ToMMo:0.810
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.845

Prediction

ClinVar

Clinical Significance
Review star [No Data.]
Show details
Links
Type Database ID Link
Gene MIM 603347 OMIM
HGNC 7895 HGNC
Ensembl ENSG00000170485 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv7954563 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
[No Data.]
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.002 breast carcinoma However, when accounting for potential effect modification, rs23051560 (Ala394Th... BeFree 22473669 Detail
0.009 Malignant neoplasm of breast However, when accounting for potential effect modification, rs23051560 (Ala394Th... BeFree 22473669 Detail
<0.001 lymphoma Ala394Thr polymorphism in the clock gene NPAS2: a circadian modifier for the ris... BeFree 17096334 Detail
<0.001 chronic lymphocytic leukemia Lack of association of the NPAS2 gene Ala394Thr polymorphism (rs2305160:G&gt;A) ... BeFree 25227809 Detail
<0.001 lymphoma Ala394Thr polymorphism in the clock gene NPAS2: a circadian modifier for the ris... BeFree 17096334 Detail
Annotation

Annotations

DescrptionSourceLinks
However, when accounting for potential effect modification, rs23051560 (Ala394Thr) in the largest ci... DisGeNET Detail
However, when accounting for potential effect modification, rs23051560 (Ala394Thr) in the largest ci... DisGeNET Detail
Ala394Thr polymorphism in the clock gene NPAS2: a circadian modifier for the risk of non-Hodgkin's l... DisGeNET Detail
Lack of association of the NPAS2 gene Ala394Thr polymorphism (rs2305160:G&gt;A) with risk of chronic... DisGeNET Detail
Ala394Thr polymorphism in the clock gene NPAS2: a circadian modifier for the risk of non-Hodgkin's l... DisGeNET 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
-
Genome
hg38
Position
chr2:100,974,842-100,974,842
Variant Type
snv
Reference Allele
A
Alternative Allele
G
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1111
Mean of sample read depth (HGVD)
14.28
Standard deviation of sample read depth (HGVD)
15.88
Number of reference allele (HGVD)
392
Number of alternative allele (HGVD)
1827
Allele Frequency (HGVD)
0.8233438485804416
Gene Symbol (HGVD)
NPAS2
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))
rs2305160
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.8101
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
13577
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)
7304
East Asian Heterozygous Counts (ExAC)
1104
East Asian Homozygous Counts (ExAC)
3100
East Asian Allele Frequency (ExAC)
0.8449791763072652
Chromosome Counts in All Race (ExAC)
121290
Allele Counts in All Race (ExAC)
85781
Heterozygous Counts in All Race (ExAC)
24261
Homozygous Counts in All Race (ExAC)
30760
Allele Frequency in All Race (ExAC)
0.7072388490394921
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