chr3:57138419:G>A Detail (hg19) (IL17RD)

Information

Genome

Assembly Position
hg19 chr3:57,138,419-57,138,419
hg38 chr3:57,104,391-57,104,391 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_017563.4:c.764C>T NP_060033.3:p.Thr255Met
NM_001318864.1:c.332C>T NP_001305793.1:p.Thr111Met
Ensemble ENST00000296318.12:c.764C>T ENST00000296318.12:p.Thr255Met
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.155
ToMMo:0.159
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.145

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 606807 OMIM
HGNC 17616 HGNC
Ensembl ENSG00000144730 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv12632046 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2024-01-31 criteria provided, multiple submitters, no conflicts not provided germline Detail
Benign 2021-08-19 criteria provided, single submitter hypogonadotropic hypogonadism 18 with or without anosmia germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
<0.001 anemia Meanwhile, individuals with the hHbS rs334 TT, IL10 rs3024500 AA, and IL17RD rs6... BeFree 24312262 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_017563.5(IL17RD):c.764C>T (p.Thr255Met) AND not provided ClinVar Detail
NM_017563.5(IL17RD):c.764C>T (p.Thr255Met) AND Hypogonadotropic hypogonadism 18 with or without anos... ClinVar Detail
Meanwhile, individuals with the hHbS rs334 TT, IL10 rs3024500 AA, and IL17RD rs6780995 GA genotypes ... 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
rs6780995 dbSNP
Genome
hg19
Position
chr3:57,138,419-57,138,419
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
94.02
Standard deviation of sample read depth (HGVD)
42.07
Number of reference allele (HGVD)
2046
Number of alternative allele (HGVD)
374
Allele Frequency (HGVD)
0.15454545454545454
Gene Symbol (HGVD)
IL17RD
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))
rs6780995
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.1594
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
2671
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
7232
East Asian Allele Counts (ExAC)
1050
East Asian Heterozygous Counts (ExAC)
918
East Asian Homozygous Counts (ExAC)
66
East Asian Allele Frequency (ExAC)
0.14518805309734514
Chromosome Counts in All Race (ExAC)
112576
Allele Counts in All Race (ExAC)
73062
Heterozygous Counts in All Race (ExAC)
24382
Homozygous Counts in All Race (ExAC)
24340
Allele Frequency in All Race (ExAC)
0.6490015633882888
Genome browser