chr19:39735106:T>C Detail (hg19) (IFNL3)

Information

Genome

Assembly Position
hg19 chr19:39,735,106-39,735,106
hg38 chr19:39,244,466-39,244,466 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_172139.2:c.209A>G NP_742151.2:p.Lys70Arg
Ensemble ENST00000413851.3:c.209A>G ENST00000413851.3:p.Lys70Arg
ENST00000613087.5:c.221A>G ENST00000613087.5:p.Lys74Arg
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.057
ToMMo:0.103
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.058

Prediction

ClinVar

Clinical Significance Likely benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 607402 OMIM
HGNC 18365 HGNC
Ensembl ENSG00000197110 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv62049604 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Likely benign 2018-03-09 criteria provided, single submitter not specified germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.220 hepatitis C This study demonstrated that Indonesian patients with chronic hepatitis C (mostl... BeFree 24696021 Detail
0.002 Coinfection We tested the association of spontaneous clearance and three single nucleotide p... BeFree 25803108 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_172139.4(IFNL3):c.209A>G (p.Lys70Arg) AND not specified ClinVar Detail
This study demonstrated that Indonesian patients with chronic hepatitis C (mostly ethnic Java people... DisGeNET Detail
We tested the association of spontaneous clearance and three single nucleotide polymorphisms (SNPs) ... 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
rs8103142 dbSNP
Genome
hg19
Position
chr19:39,735,106-39,735,106
Variant Type
snv
Reference Allele
T
Alternative Allele
C
Filtering Status (HGVD)
PASS
Filtering Status (HGVD)
LowQual
# of samples (HGVD)
1107
Mean of sample read depth (HGVD)
29.96
Standard deviation of sample read depth (HGVD)
13.77
Number of reference allele (HGVD)
2087
Number of alternative allele (HGVD)
127
Allele Frequency (HGVD)
0.057362240289069555
Gene Symbol (HGVD)
IL28B
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))
rs8103142
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.1034
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
1732
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16756
East Asian Chromosome Counts (ExAC)
8278
East Asian Allele Counts (ExAC)
483
East Asian Heterozygous Counts (ExAC)
471
East Asian Homozygous Counts (ExAC)
6
East Asian Allele Frequency (ExAC)
0.0583474269147137
Chromosome Counts in All Race (ExAC)
103340
Allele Counts in All Race (ExAC)
28797
Heterozygous Counts in All Race (ExAC)
20747
Homozygous Counts in All Race (ExAC)
4025
Allele Frequency in All Race (ExAC)
0.27866266692471453
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