chr16:50745199:C>T Detail (hg19) (NOD2)

Information

Genome

Assembly Position
hg19 chr16:50,745,199-50,745,199
hg38 chr16:50,711,288-50,711,288 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_001293557.1:c.1377C>T NP_001280486.1:p.Arg459=
NM_022162.2:c.1377C>T NP_071445.1:p.Arg459=
Ensemble ENST00000647318.2:c.1296C>T ENST00000647318.2:p.Arg432=
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.001
ToMMo:<0.001
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.007

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 605956 OMIM
HGNC 5331 HGNC
Ensembl ENSG00000167207 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv55472545 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2018-01-13 criteria provided, single submitter Blau syndrome germline Detail
Benign 2023-11-12 criteria provided, multiple submitters, no conflicts not specified germline Detail
Benign 2018-01-13 criteria provided, single submitter inflammatory bowel disease 1 germline Detail
Benign 2023-11-29 criteria provided, single submitter not provided germline Detail
Benign 2024-02-01 criteria provided, single submitter Blau syndrome,Regional enteritis germline Detail
Benign 2024-02-01 criteria provided, single submitter Blau syndrome,Regional enteritis germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.560 Crohn Disease The NOD2 single nucleotide polymorphisms rs2066843 and rs2076756 are novel and c... BeFree 21209938 Detail
0.002 pathologic fistula In CD patients homozygous for these novel NOD2 variants, genotype-phenotype anal... BeFree 21209938 Detail
0.234 ulcerative colitis Genomic DNA from 2700 Caucasians including 812 patients with Crohn's disease (CD... BeFree 21209938 Detail
0.397 Inflammatory Bowel Diseases The aims were to analyze two novel NOD2 variants (rs2066843 and rs2076756) in a ... BeFree 21209938 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_001370466.1(NOD2):c.1296C>T (p.Arg432=) AND Blau syndrome ClinVar Detail
NM_001370466.1(NOD2):c.1296C>T (p.Arg432=) AND not specified ClinVar Detail
NM_001370466.1(NOD2):c.1296C>T (p.Arg432=) AND Inflammatory bowel disease 1 ClinVar Detail
NM_001370466.1(NOD2):c.1296C>T (p.Arg432=) AND not provided ClinVar Detail
NM_001370466.1(NOD2):c.1296C>T (p.Arg432=) AND multiple conditions ClinVar Detail
NM_001370466.1(NOD2):c.1296C>T (p.Arg432=) AND multiple conditions ClinVar Detail
The NOD2 single nucleotide polymorphisms rs2066843 and rs2076756 are novel and common Crohn's diseas... DisGeNET Detail
In CD patients homozygous for these novel NOD2 variants, genotype-phenotype analysis revealed higher... DisGeNET Detail
Genomic DNA from 2700 Caucasians including 812 patients with Crohn's disease (CD), 442 patients with... DisGeNET Detail
The aims were to analyze two novel NOD2 variants (rs2066843 and rs2076756) in a large cohort of pati... 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
-
dbSNP
rs2066843 dbSNP
Genome
hg19
Position
chr16:50,745,199-50,745,199
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
Filtering Status (HGVD)
LowQual
# of samples (HGVD)
1209
Mean of sample read depth (HGVD)
179.04
Standard deviation of sample read depth (HGVD)
82.58
Number of reference allele (HGVD)
2415
Number of alternative allele (HGVD)
3
Allele Frequency (HGVD)
0.0012406947890818859
Gene Symbol (HGVD)
NOD2
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))
rs2066843
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0004
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
7
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16758
East Asian Chromosome Counts (ExAC)
8602
East Asian Allele Counts (ExAC)
57
East Asian Heterozygous Counts (ExAC)
57
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
0.006626365961404325
Chromosome Counts in All Race (ExAC)
120126
Allele Counts in All Race (ExAC)
22391
Heterozygous Counts in All Race (ExAC)
17139
Homozygous Counts in All Race (ExAC)
2626
Allele Frequency in All Race (ExAC)
0.18639595091820255
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