chr22:36862461:T>C Detail (hg38) (NCF4, NCF4-AS1)

Information

Genome

Assembly Position
hg19 chr22:37,258,503-37,258,503 View the variant detail on this assembly version.
hg38 chr22:36,862,461-36,862,461

HGVS

Type Transcript Protein
RefSeq NM_000631.4:c.32+1258T>C
NM_013416.3:c.32+1258T>C
Ensemble ENST00000248899.11:c.32+1258T>C
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:0.133
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:[No Data.]

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 601488 OMIM
HGNC 7662 HGNC
Ensembl ENSG00000100365 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv65873156 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2024-01-02 criteria provided, single submitter Granulomatous disease, chronic, autosomal recessive, cytochrome b-positive, type 3 germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.003 Inflammatory Bowel Diseases NCF4 and IRGM were significantly associated with ileal CD (P-value(rs4821544)=0.... BeFree 18580884 Detail
0.002 Dermatitis, Atopic [Meta-analysis of genome-wide association studies identifies three new risk loci... GAD 22197932 Detail
0.003 Inflammatory Bowel Diseases [A genome-wide association study identifies IL23R as an inflammatory bowel disea... GAD 17068223 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000631.5(NCF4):c.32+1258T>C AND Granulomatous disease, chronic, autosomal recessive, cytochrome b... ClinVar Detail
NCF4 and IRGM were significantly associated with ileal CD (P-value(rs4821544)=0.0090, odds ratio (OR... DisGeNET Detail
[Meta-analysis of genome-wide association studies identifies three new risk loci for atopic dermatit... DisGeNET Detail
[A genome-wide association study identifies IL23R as an inflammatory bowel disease gene.] DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs4821544 dbSNP
Genome
hg38
Position
chr22:36,862,461-36,862,461
Variant Type
snv
Reference Allele
T
Alternative Allele
C
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))
rs4821544
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.1327
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
2224
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
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