chr2:218385280:G>C Detail (hg38) (SLC11A1)

Information

Genome

Assembly Position
hg19 chr2:219,250,003-219,250,003 View the variant detail on this assembly version.
hg38 chr2:218,385,280-218,385,280

HGVS

Type Transcript Protein
RefSeq NM_000578.3:c.393+14G>C
Ensemble ENST00000233202.11:c.393+14G>C
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.152
ToMMo:0.135
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.119

Prediction

ClinVar

Clinical Significance
Review star [No Data.]
Show details
Links
Type Database ID Link
Gene MIM 600266 OMIM
HGNC 10907 HGNC
Ensembl ENSG00000018280 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv10529114 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
<0.001 rheumatoid arthritis We analysed four NRAMP1 gene polymorphisms including 5' promoter (GT)(n) (rs3444... BeFree 19055603 Detail
<0.001 Active tuberculosis Multilocus analyses between polymorphisms in SLC11A1 and 11 TB candidate genes d... BeFree 19723394 Detail
<0.001 Active tuberculosis Multilocus analyses between polymorphisms in SLC11A1 and 11 TB candidate genes d... BeFree 19723394 Detail
<0.001 Active tuberculosis SLC11A1 polymorphism rs3731865 was associated with TB in African-Americans, cons... BeFree 19723394 Detail
Annotation

Annotations

DescrptionSourceLinks
We analysed four NRAMP1 gene polymorphisms including 5' promoter (GT)(n) (rs34448891), INT4 (469 + 1... DisGeNET Detail
Multilocus analyses between polymorphisms in SLC11A1 and 11 TB candidate genes detected interactions... DisGeNET Detail
Multilocus analyses between polymorphisms in SLC11A1 and 11 TB candidate genes detected interactions... DisGeNET Detail
SLC11A1 polymorphism rs3731865 was associated with TB in African-Americans, consistent with previous... DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
Genome
hg38
Position
chr2:218,385,280-218,385,280
Variant Type
snv
Reference Allele
G
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
837
Mean of sample read depth (HGVD)
118.11
Standard deviation of sample read depth (HGVD)
56.70
Number of reference allele (HGVD)
1420
Number of alternative allele (HGVD)
254
Allele Frequency (HGVD)
0.15173237753882915
Gene Symbol (HGVD)
SLC11A1
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))
rs3731865
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.1352
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
2266
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8634
East Asian Allele Counts (ExAC)
1026
East Asian Heterozygous Counts (ExAC)
874
East Asian Homozygous Counts (ExAC)
76
East Asian Allele Frequency (ExAC)
0.11883252258512857
Chromosome Counts in All Race (ExAC)
121022
Allele Counts in All Race (ExAC)
27633
Heterozygous Counts in All Race (ExAC)
20597
Homozygous Counts in All Race (ExAC)
3518
Allele Frequency in All Race (ExAC)
0.2283303862107716
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