chr6:52051274:G>A Detail (hg19) (IL17A)

Information

Genome

Assembly Position
hg19 chr6:52,051,274-52,051,274
hg38 chr6:52,186,476-52,186,476 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq
Ensemble ENST00000648244.1:c.27+18G>A
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.241
ToMMo:0.243
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.195

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 603149 OMIM
HGNC 5981 HGNC
Ensembl ENSG00000112115 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv25369786 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2018-11-12 criteria provided, single submitter not provided germline Detail
Benign 2024-01-24 criteria provided, single submitter not specified germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.002 Graves Disease In conclusion, the results indicate that IL-17F/rs763780 polymorphisms may affec... BeFree 22816799 Detail
<0.001 Graves Disease In conclusion, the results indicate that IL-17F/rs763780 polymorphisms may affec... BeFree 22816799 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_002190.3(IL17A):c.27+18G>A AND not provided ClinVar Detail
NM_002190.3(IL17A):c.27+18G>A AND not specified ClinVar Detail
In conclusion, the results indicate that IL-17F/rs763780 polymorphisms may affect the susceptibility... DisGeNET Detail
In conclusion, the results indicate that IL-17F/rs763780 polymorphisms may affect the susceptibility... DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs3819025 dbSNP
Genome
hg19
Position
chr6:52,051,274-52,051,274
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
837
Mean of sample read depth (HGVD)
51.41
Standard deviation of sample read depth (HGVD)
21.56
Number of reference allele (HGVD)
1271
Number of alternative allele (HGVD)
403
Allele Frequency (HGVD)
0.24074074074074073
Gene Symbol (HGVD)
IL17A
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))
rs3819025
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.2427
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
4068
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8508
East Asian Allele Counts (ExAC)
1656
East Asian Heterozygous Counts (ExAC)
1344
East Asian Homozygous Counts (ExAC)
156
East Asian Allele Frequency (ExAC)
0.19464033850493653
Chromosome Counts in All Race (ExAC)
120650
Allele Counts in All Race (ExAC)
14070
Heterozygous Counts in All Race (ExAC)
10400
Homozygous Counts in All Race (ExAC)
1835
Allele Frequency in All Race (ExAC)
0.11661831744716121
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