chr3:9960070:C>T Detail (hg19) (IL17RC)

Information

Genome

Assembly Position
hg19 chr3:9,960,070-9,960,070
hg38 chr3:9,918,386-9,918,386 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_153461.3:c.545C>T NP_703191.1:p.Ser182Leu
NM_032732.5:c.332C>T NP_116121.2:p.Ser111Leu
NM_153460.3:c.332C>T NP_703190.1:p.Ser111Leu
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.087
ToMMo:0.082
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.116

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 610925 OMIM
HGNC 18358 HGNC
Ensembl ENSG00000163702 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv11430514 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2024-02-01 criteria provided, multiple submitters, no conflicts Candidiasis, familial, 9 germline Detail
not provided no assertion provided not provided unknown Detail
Benign 2024-01-24 criteria provided, single submitter not specified germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
<0.001 anemia Furthermore, IL17RE rs708567 GA and hHbS rs334 AT individuals were associated wi... BeFree 24312262 Detail
<0.001 malaria Furthermore, IL17RE rs708567 GA and hHbS rs334 AT individuals were associated wi... BeFree 24312262 Detail
<0.001 Parasitemia Genotype-phenotype correlations between SNPs and clinical parameters revealed th... BeFree 22673309 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_153460.4(IL17RC):c.332C>T (p.Ser111Leu) AND Candidiasis, familial, 9 ClinVar Detail
NM_153460.4(IL17RC):c.332C>T (p.Ser111Leu) AND not provided ClinVar Detail
NM_153460.4(IL17RC):c.332C>T (p.Ser111Leu) AND not specified ClinVar Detail
Furthermore, IL17RE rs708567 GA and hHbS rs334 AT individuals were associated with protection from u... DisGeNET Detail
Furthermore, IL17RE rs708567 GA and hHbS rs334 AT individuals were associated with protection from u... DisGeNET Detail
Genotype-phenotype correlations between SNPs and clinical parameters revealed that genotypes of rs70... 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
rs708567 dbSNP
Genome
hg19
Position
chr3:9,960,070-9,960,070
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1205
Mean of sample read depth (HGVD)
89.74
Standard deviation of sample read depth (HGVD)
45.29
Number of reference allele (HGVD)
2200
Number of alternative allele (HGVD)
210
Allele Frequency (HGVD)
0.08713692946058091
Gene Symbol (HGVD)
IL17RC
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))
rs708567
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0815
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
1366
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
5480
East Asian Allele Counts (ExAC)
634
East Asian Heterozygous Counts (ExAC)
586
East Asian Homozygous Counts (ExAC)
24
East Asian Allele Frequency (ExAC)
0.11569343065693431
Chromosome Counts in All Race (ExAC)
100078
Allele Counts in All Race (ExAC)
51227
Heterozygous Counts in All Race (ExAC)
26085
Homozygous Counts in All Race (ExAC)
12571
Allele Frequency in All Race (ExAC)
0.5118707408221587
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