chr4:102612664:T>A Detail (hg38) (NFKB1)

Information

Genome

Assembly Position
hg19 chr4:103,533,821-103,533,821 View the variant detail on this assembly version.
hg38 chr4:102,612,664-102,612,664

HGVS

Type Transcript Protein
RefSeq NM_003998.3:c.2592+58T>A
NM_001165412.1:c.2589+58T>A
NM_001319226.1:c.2589+58T>A
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:0.084
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 164011 OMIM
HGNC 7794 HGNC
Ensembl ENSG00000109320 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv18082253 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2021-06-19 criteria provided, single submitter not provided germline Detail
Benign 2023-11-12 criteria provided, single submitter not specified germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.005 Malignant tumor of colon The most significant finding (nominal P = 0.0004; false discovery rate q = 0.037... BeFree 21129206 Detail
0.007 Malignant tumor of colon The most significant finding (nominal P = 0.0004; false discovery rate q = 0.037... BeFree 21129206 Detail
0.006 colon carcinoma The most significant finding (nominal P = 0.0004; false discovery rate q = 0.037... BeFree 21129206 Detail
0.007 colon carcinoma The most significant finding (nominal P = 0.0004; false discovery rate q = 0.037... BeFree 21129206 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_003998.4(NFKB1):c.2592+58T>A AND not provided ClinVar Detail
NM_003998.4(NFKB1):c.2592+58T>A AND not specified ClinVar Detail
The most significant finding (nominal P = 0.0004; false discovery rate q = 0.037) was a combined gen... DisGeNET Detail
The most significant finding (nominal P = 0.0004; false discovery rate q = 0.037) was a combined gen... DisGeNET Detail
The most significant finding (nominal P = 0.0004; false discovery rate q = 0.037) was a combined gen... DisGeNET Detail
The most significant finding (nominal P = 0.0004; false discovery rate q = 0.037) was a combined gen... DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs4648110 dbSNP
Genome
hg38
Position
chr4:102,612,664-102,612,664
Variant Type
snv
Reference Allele
T
Alternative Allele
A
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))
rs4648110
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0843
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
1413
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
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