chr5:35871088:G>A Detail (hg38) (IL7R)

Information

Genome

Assembly Position
hg19 chr5:35,871,190-35,871,190 View the variant detail on this assembly version.
hg38 chr5:35,871,088-35,871,088

HGVS

Type Transcript Protein
RefSeq NM_002185.3:c.412G>A NP_002176.2:p.Val138Ile
Ensemble ENST00000303115.8:c.412G>A ENST00000303115.8:p.Val138Ile
ENST00000506850.5:c.412G>A ENST00000506850.5:p.Val138Ile
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.489
ToMMo:0.477
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.474

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 146661 OMIM
HGNC 6024 HGNC
Ensembl ENSG00000168685 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv20784107 TogoVar
COSMIC COSM149814 COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2024-01-23 reviewed by expert panel Immunodeficiency 104 germline unknown Detail
Benign 2024-01-24 criteria provided, multiple submitters, no conflicts not specified germline Detail
Benign 2015-03-03 criteria provided, single submitter not provided germline unknown Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.004 Lymphoma, Large-Cell, Follicular A significant interaction with BMI was only observed for IFNGR2 (rs9808753 P(for... BeFree 20952689 Detail
0.003 B-Cell Lymphomas A significant interaction with BMI was only observed for IFNGR2 (rs9808753 P(for... BeFree 20952689 Detail
0.006 Mucosa-Associated Lymphoid Tissue Lymphoma After stratification by common B-cell lymphoma subtypes, a significant interacti... BeFree 20952689 Detail
0.050 Lymphoma, Non-Hodgkin A significant interaction with BMI was only observed for IFNGR2 (rs9808753 P(for... BeFree 20952689 Detail
0.021 chronic lymphocytic leukemia After stratification by common B-cell lymphoma subtypes, a significant interacti... BeFree 20952689 Detail
0.010 B-Cell Lymphomas A significant interaction with BMI was only observed for IFNGR2 (rs9808753 P(for... BeFree 20952689 Detail
0.004 T-Cell Lymphoma A significant interaction with BMI was only observed for IFNGR2 (rs9808753 P(for... BeFree 20952689 Detail
0.007 Lymphoma, Follicular After stratification by common B-cell lymphoma subtypes, a significant interacti... BeFree 20952689 Detail
0.002 T-Cell Lymphoma A significant interaction with BMI was only observed for IFNGR2 (rs9808753 P(for... BeFree 20952689 Detail
0.360 Severe Combined Immunodeficiency, Autosomal Recessive, T Cell Negative, B Cell Positive, NK Cell Positive NA CLINVAR Detail
Annotation

Annotations

DescrptionSourceLinks
NM_002185.5(IL7R):c.412G>A (p.Val138Ile) AND Immunodeficiency 104 ClinVar Detail
NM_002185.5(IL7R):c.412G>A (p.Val138Ile) AND not specified ClinVar Detail
NM_002185.5(IL7R):c.412G>A (p.Val138Ile) AND not provided ClinVar Detail
A significant interaction with BMI was only observed for IFNGR2 (rs9808753 P(forinteraction) = .034)... DisGeNET Detail
A significant interaction with BMI was only observed for IFNGR2 (rs9808753 P(forinteraction) = .034)... DisGeNET Detail
After stratification by common B-cell lymphoma subtypes, a significant interaction was observed for ... DisGeNET Detail
A significant interaction with BMI was only observed for IFNGR2 (rs9808753 P(forinteraction) = .034)... DisGeNET Detail
After stratification by common B-cell lymphoma subtypes, a significant interaction was observed for ... DisGeNET Detail
A significant interaction with BMI was only observed for IFNGR2 (rs9808753 P(forinteraction) = .034)... DisGeNET Detail
A significant interaction with BMI was only observed for IFNGR2 (rs9808753 P(forinteraction) = .034)... DisGeNET Detail
After stratification by common B-cell lymphoma subtypes, a significant interaction was observed for ... DisGeNET Detail
A significant interaction with BMI was only observed for IFNGR2 (rs9808753 P(forinteraction) = .034)... DisGeNET Detail
NA 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
rs1494555 dbSNP
Genome
hg38
Position
chr5:35,871,088-35,871,088
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1188
Mean of sample read depth (HGVD)
30.65
Standard deviation of sample read depth (HGVD)
16.31
Number of reference allele (HGVD)
1214
Number of alternative allele (HGVD)
1162
Allele Frequency (HGVD)
0.4890572390572391
Gene Symbol (HGVD)
IL7R
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))
rs1494555
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.4771
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
7996
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8642
East Asian Allele Counts (ExAC)
4097
East Asian Heterozygous Counts (ExAC)
2165
East Asian Homozygous Counts (ExAC)
966
East Asian Allele Frequency (ExAC)
0.47408007405693126
Chromosome Counts in All Race (ExAC)
121272
Allele Counts in All Race (ExAC)
79061
Heterozygous Counts in All Race (ExAC)
25959
Homozygous Counts in All Race (ExAC)
26551
Allele Frequency in All Race (ExAC)
0.6519311959891814
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