chr2:219254750:C>T Detail (hg19) (SLC11A1)

Information

Genome

Assembly Position
hg19 chr2:219,254,750-219,254,750
hg38 chr2:218,390,027-218,390,027 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_000578.3:c.953C>T NP_000569.3:p.Ala318Val
Ensemble ENST00000233202.11:c.953C>T ENST00000233202.11:p.Ala318Val
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:0.004

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 tgv10529443 TogoVar
COSMIC COSM6779221 COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
[No Data.]
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.124 HIV Infections To study the variations in the NRAMP1 gene using five genotypes (274C/T, 577-18G... BeFree 12019922 Detail
Annotation

Annotations

DescrptionSourceLinks
To study the variations in the NRAMP1 gene using five genotypes (274C/T, 577-18G/A, A318V, D543N and... 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
-
Genome
hg19
Position
chr2:219,254,750-219,254,750
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
Filtering Status (HGVD)
LowQual
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
75.24
Standard deviation of sample read depth (HGVD)
34.95
Number of reference allele (HGVD)
2419
Number of alternative allele (HGVD)
1
Allele Frequency (HGVD)
4.1322314049586776E-4
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))
rs201565523
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)
8620
East Asian Allele Counts (ExAC)
36
East Asian Heterozygous Counts (ExAC)
36
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
0.004176334106728539
Chromosome Counts in All Race (ExAC)
116924
Allele Counts in All Race (ExAC)
38
Heterozygous Counts in All Race (ExAC)
38
Homozygous Counts in All Race (ExAC)
0
Allele Frequency in All Race (ExAC)
3.249974342307824E-4
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