chr5:35861068:T>C Detail (hg19) (IL7R)

Information

Genome

Assembly Position
hg19 chr5:35,861,068-35,861,068
hg38 chr5:35,860,966-35,860,966 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_002185.3:c.197T>C NP_002176.2:p.Ile66Thr
Ensemble ENST00000303115.8:c.197T>C ENST00000303115.8:p.Ile66Thr
ENST00000506850.5:c.197T>C ENST00000506850.5:p.Ile66Thr
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.413
ToMMo:0.419
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.423

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 tgv20783761 TogoVar
COSMIC COSM149813 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
0.360 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.197T>C (p.Ile66Thr) AND Immunodeficiency 104 ClinVar Detail
NM_002185.5(IL7R):c.197T>C (p.Ile66Thr) AND not specified ClinVar Detail
NM_002185.5(IL7R):c.197T>C (p.Ile66Thr) AND not provided ClinVar 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
rs1494558 dbSNP
Genome
hg19
Position
chr5:35,861,068-35,861,068
Variant Type
snv
Reference Allele
T
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1138
Mean of sample read depth (HGVD)
42.95
Standard deviation of sample read depth (HGVD)
32.26
Number of reference allele (HGVD)
1336
Number of alternative allele (HGVD)
939
Allele Frequency (HGVD)
0.41274725274725277
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))
rs1494558
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.4185
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
7014
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8632
East Asian Allele Counts (ExAC)
3652
East Asian Heterozygous Counts (ExAC)
2104
East Asian Homozygous Counts (ExAC)
774
East Asian Allele Frequency (ExAC)
0.4230769230769231
Chromosome Counts in All Race (ExAC)
121330
Allele Counts in All Race (ExAC)
76179
Heterozygous Counts in All Race (ExAC)
26907
Homozygous Counts in All Race (ExAC)
24636
Allele Frequency in All Race (ExAC)
0.6278661501689606
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