chr22:37469591:G>A Detail (hg19) (TMPRSS6)

Information

Genome

Assembly Position
hg19 chr22:37,469,591-37,469,591
hg38 chr22:37,073,551-37,073,551 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_153609.3:c.1536C>T NP_705837.1:p.Asp512=
NM_001289001.1:c.1536C>T NP_001275930.1:p.Asp512=
NM_001289000.1:c.1536C>T NP_001275929.1:p.Asp512=
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.462
ToMMo:0.448
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.476

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 609862 OMIM
HGNC 16517 HGNC
Ensembl ENSG00000187045 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv65880881 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign criteria provided, single submitter not specified germline Detail
Benign 2018-01-13 criteria provided, single submitter microcytic anemia germline Detail
Benign 2024-01-31 criteria provided, multiple submitters, no conflicts not provided germline Detail
Benign 2021-10-20 criteria provided, multiple submitters, no conflicts Iron-refractory iron deficiency anemia germline unknown Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
<0.001 hemochromatosis As part of the Healthy Ageing across the Life Course (HALCyon) program, men and ... BeFree 23468552 Detail
<0.001 hemochromatosis As part of the Healthy Ageing across the Life Course (HALCyon) program, men and ... BeFree 23468552 Detail
<0.001 hemochromatosis As part of the Healthy Ageing across the Life Course (HALCyon) program, men and ... BeFree 23468552 Detail
<0.001 hemochromatosis As part of the Healthy Ageing across the Life Course (HALCyon) program, men and ... BeFree 23468552 Detail
0.003 iron deficiency anemia To evaluate the association of genetic variants in genes involved in iron delive... BeFree 22323359 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_001374504.1(TMPRSS6):c.1536C>T (p.Asp512=) AND not specified ClinVar Detail
NM_001374504.1(TMPRSS6):c.1536C>T (p.Asp512=) AND Microcytic anemia ClinVar Detail
NM_001374504.1(TMPRSS6):c.1536C>T (p.Asp512=) AND not provided ClinVar Detail
NM_001374504.1(TMPRSS6):c.1536C>T (p.Asp512=) AND Iron-refractory iron deficiency anemia ClinVar Detail
As part of the Healthy Ageing across the Life Course (HALCyon) program, men and women aged between 4... DisGeNET Detail
As part of the Healthy Ageing across the Life Course (HALCyon) program, men and women aged between 4... DisGeNET Detail
As part of the Healthy Ageing across the Life Course (HALCyon) program, men and women aged between 4... DisGeNET Detail
As part of the Healthy Ageing across the Life Course (HALCyon) program, men and women aged between 4... DisGeNET Detail
To evaluate the association of genetic variants in genes involved in iron delivery and hepcidin regu... 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
-
dbSNP
rs4820268 dbSNP
Genome
hg19
Position
chr22:37,469,591-37,469,591
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
153.46
Standard deviation of sample read depth (HGVD)
71.60
Number of reference allele (HGVD)
1303
Number of alternative allele (HGVD)
1117
Allele Frequency (HGVD)
0.4615702479338843
Gene Symbol (HGVD)
TMPRSS6
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))
rs4820268
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.4479
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
7506
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8594
East Asian Allele Counts (ExAC)
4091
East Asian Heterozygous Counts (ExAC)
2153
East Asian Homozygous Counts (ExAC)
969
East Asian Allele Frequency (ExAC)
0.47602978822434255
Chromosome Counts in All Race (ExAC)
121322
Allele Counts in All Race (ExAC)
65395
Heterozygous Counts in All Race (ExAC)
29419
Homozygous Counts in All Race (ExAC)
17988
Allele Frequency in All Race (ExAC)
0.539020128253738
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