chr2:190444630:C>G Detail (hg19) (SLC40A1)

Information

Genome

Assembly Position
hg19 chr2:190,444,630-190,444,630
hg38 chr2:189,579,904-189,579,904 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_014585.5:c.44-24G>C
Ensemble ENST00000261024.7:c.44-24G>C
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.869
ToMMo:0.861
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.845

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 604653 OMIM
HGNC 10909 HGNC
Ensembl ENSG00000138449 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv9898008 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2024-01-18 criteria provided, multiple submitters, no conflicts hemochromatosis type 4 germline unknown Detail
Benign 2018-11-12 criteria provided, single submitter not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.003 Hereditary hemochromatosis Our results make it likely the role of rs10421768, rs235756, rs2230267 and rs143... BeFree 25976471 Detail
<0.001 Hereditary hemochromatosis We investigated 6 polymorphisms (rs10421768 in HAMP gene, rs235756 in BMP2 gene,... BeFree 25976471 Detail
0.125 Hereditary hemochromatosis We investigated 6 polymorphisms (rs10421768 in HAMP gene, rs235756 in BMP2 gene,... BeFree 25976471 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_014585.6(SLC40A1):c.44-24G>C AND Hemochromatosis type 4 ClinVar Detail
NM_014585.6(SLC40A1):c.44-24G>C AND not provided ClinVar Detail
Our results make it likely the role of rs10421768, rs235756, rs2230267 and rs1439816 polymorphisms, ... DisGeNET Detail
We investigated 6 polymorphisms (rs10421768 in HAMP gene, rs235756 in BMP2 gene, rs2230267 in FTL ge... DisGeNET Detail
We investigated 6 polymorphisms (rs10421768 in HAMP gene, rs235756 in BMP2 gene, rs2230267 in FTL ge... DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs1439816 dbSNP
Genome
hg19
Position
chr2:190,444,630-190,444,630
Variant Type
snv
Reference Allele
C
Alternative Allele
G
Filtering Status (HGVD)
PASS
# of samples (HGVD)
837
Mean of sample read depth (HGVD)
36.10
Standard deviation of sample read depth (HGVD)
18.51
Number of reference allele (HGVD)
220
Number of alternative allele (HGVD)
1454
Allele Frequency (HGVD)
0.8685782556750299
Gene Symbol (HGVD)
SLC40A1
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))
rs1439816
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.861
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
14431
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8604
East Asian Allele Counts (ExAC)
7270
East Asian Heterozygous Counts (ExAC)
1168
East Asian Homozygous Counts (ExAC)
3051
East Asian Allele Frequency (ExAC)
0.8449558344955834
Chromosome Counts in All Race (ExAC)
120768
Allele Counts in All Race (ExAC)
95063
Heterozygous Counts in All Race (ExAC)
18133
Homozygous Counts in All Race (ExAC)
38465
Allele Frequency in All Race (ExAC)
0.7871538818229995
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