chr16:50712018:C>T Detail (hg38) (NOD2)

Information

Genome

Assembly Position
hg19 chr16:50,745,929-50,745,929 View the variant detail on this assembly version.
hg38 chr16:50,712,018-50,712,018

HGVS

Type Transcript Protein
RefSeq NM_001293557.1:c.2107C>T NP_001280486.1:p.Arg703Cys
NM_022162.2:c.2107C>T NP_071445.1:p.Arg703Cys
Ensemble ENST00000300589.6:c.2107C>T ENST00000300589.6:p.Arg703Cys
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.002
ToMMo:<0.001
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.001

Prediction

ClinVar

Clinical Significance Conflicting classifications of pathogenicity
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 tgv55472734 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Likely benign 2014-10-24 criteria provided, single submitter not specified germline Detail
Likely benign 2017-04-27 criteria provided, single submitter Blau syndrome germline Detail
Conflicting interpretations of pathogenicity 2024-04-01 criteria provided, conflicting interpretations not provided germline Detail
Likely benign 2017-04-27 criteria provided, single submitter inflammatory bowel disease 1 germline Detail
Uncertain significance 2022-05-03 criteria provided, single submitter Autoinflammatory syndrome germline Detail
Likely benign 2024-01-31 criteria provided, single submitter Regional enteritis,Blau syndrome germline Detail
Likely benign 2024-01-31 criteria provided, single submitter Regional enteritis,Blau syndrome germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.028 Ileal Diseases These results confirm that variant NOD2/CARD15 (R702W, R703C and 3020insC) allel... BeFree 15770725 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_001370466.1(NOD2):c.2026C>T (p.Arg676Cys) AND not specified ClinVar Detail
NM_001370466.1(NOD2):c.2026C>T (p.Arg676Cys) AND Blau syndrome ClinVar Detail
NM_001370466.1(NOD2):c.2026C>T (p.Arg676Cys) AND not provided ClinVar Detail
NM_001370466.1(NOD2):c.2026C>T (p.Arg676Cys) AND Inflammatory bowel disease 1 ClinVar Detail
NM_001370466.1(NOD2):c.2026C>T (p.Arg676Cys) AND Autoinflammatory syndrome ClinVar Detail
NM_001370466.1(NOD2):c.2026C>T (p.Arg676Cys) AND multiple conditions ClinVar Detail
NM_001370466.1(NOD2):c.2026C>T (p.Arg676Cys) AND multiple conditions ClinVar Detail
These results confirm that variant NOD2/CARD15 (R702W, R703C and 3020insC) alleles are associated wi... 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
rs5743277 dbSNP
Genome
hg38
Position
chr16:50,712,018-50,712,018
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
Filtering Status (HGVD)
LowQual
# of samples (HGVD)
1195
Mean of sample read depth (HGVD)
55.47
Standard deviation of sample read depth (HGVD)
26.56
Number of reference allele (HGVD)
2386
Number of alternative allele (HGVD)
4
Allele Frequency (HGVD)
0.0016736401673640166
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))
rs5743277
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0002
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
3
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8564
East Asian Allele Counts (ExAC)
11
East Asian Heterozygous Counts (ExAC)
11
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
0.0012844465203176085
Chromosome Counts in All Race (ExAC)
118864
Allele Counts in All Race (ExAC)
387
Heterozygous Counts in All Race (ExAC)
383
Homozygous Counts in All Race (ExAC)
2
Allele Frequency in All Race (ExAC)
0.0032558217795127203
Genome browser