chr17:49510457:C>T Detail (hg38) (NGFR)

Information

Genome

Assembly Position
hg19 chr17:47,587,819-47,587,819 View the variant detail on this assembly version.
hg38 chr17:49,510,457-49,510,457

HGVS

Type Transcript Protein
RefSeq NM_002507.3:c.614C>T NP_002498.1:p.Ser205Leu
Ensemble ENST00000172229.8:c.614C>T ENST00000172229.8:p.Ser205Leu
ENST00000504201.1:c.332C>T ENST00000504201.1:p.Ser111Leu
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.104
ToMMo:0.104
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.102

Prediction

ClinVar

Clinical Significance
Review star [No Data.]
Show details
Links
Type Database ID Link
Gene MIM 162010 OMIM
HGNC 7809 HGNC
Ensembl ENSG00000064300 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv58025192 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
[No Data.]
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
<0.001 Mental Depression Therefore, we examined whether a single-nucleotide polymorphism in the BDNF gene... BeFree 24047966 Detail
0.248 depressive disorder Therefore, we examined whether a single-nucleotide polymorphism in the BDNF gene... BeFree 24047966 Detail
0.003 asthma Analysis stratified by asthma-related phenotype revealed an association between ... BeFree 22468730 Detail
0.006 asthma Analysis stratified by asthma-related phenotype revealed an association between ... BeFree 22468730 Detail
<0.001 depressive disorder Therefore, we examined whether a single-nucleotide polymorphism in the BDNF gene... BeFree 24047966 Detail
0.120 Mental Depression Therefore, we examined whether a single-nucleotide polymorphism in the BDNF gene... BeFree 24047966 Detail
0.001 Unipolar Depression Previously, we reported an association between MDD and a missense polymorphism (... BeFree 21938001 Detail
<0.001 depressive disorder A missense polymorphism (S205L) of the low-affinity neurotrophin receptor p75NTR... BeFree 15274039 Detail
0.001 major depressive disorder Previously, we reported an association between MDD and a missense polymorphism (... BeFree 21938001 Detail
Annotation

Annotations

DescrptionSourceLinks
Therefore, we examined whether a single-nucleotide polymorphism in the BDNF gene (rs56164415) and re... DisGeNET Detail
Therefore, we examined whether a single-nucleotide polymorphism in the BDNF gene (rs56164415) and re... DisGeNET Detail
Analysis stratified by asthma-related phenotype revealed an association between atopy and NGFR (rs37... DisGeNET Detail
Analysis stratified by asthma-related phenotype revealed an association between atopy and NGFR (rs37... DisGeNET Detail
Therefore, we examined whether a single-nucleotide polymorphism in the BDNF gene (rs56164415) and re... DisGeNET Detail
Therefore, we examined whether a single-nucleotide polymorphism in the BDNF gene (rs56164415) and re... DisGeNET Detail
Previously, we reported an association between MDD and a missense polymorphism (Ser205Leu: rs2072446... DisGeNET Detail
A missense polymorphism (S205L) of the low-affinity neurotrophin receptor p75NTR gene is associated ... DisGeNET Detail
Previously, we reported an association between MDD and a missense polymorphism (Ser205Leu: rs2072446... 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
-
Genome
hg38
Position
chr17:49,510,457-49,510,457
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
# of samples (HGVD)
892
Mean of sample read depth (HGVD)
19.74
Standard deviation of sample read depth (HGVD)
17.85
Number of reference allele (HGVD)
1599
Number of alternative allele (HGVD)
185
Allele Frequency (HGVD)
0.10369955156950672
Gene Symbol (HGVD)
NGFR
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))
rs2072446
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.1035
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
1734
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8626
East Asian Allele Counts (ExAC)
882
East Asian Heterozygous Counts (ExAC)
790
East Asian Homozygous Counts (ExAC)
46
East Asian Allele Frequency (ExAC)
0.10224901460700209
Chromosome Counts in All Race (ExAC)
120822
Allele Counts in All Race (ExAC)
6216
Heterozygous Counts in All Race (ExAC)
5794
Homozygous Counts in All Race (ExAC)
211
Allele Frequency in All Race (ExAC)
0.05144758404926255
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