chr11:63487386:T>C Detail (hg19) (RTN3)

Information

Genome

Assembly Position
hg19 chr11:63,487,386-63,487,386
hg38 chr11:63,719,914-63,719,914 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_201430.2:c.143-30077T>C
NR_049751.1:c.143-30077T>C
NM_001265589.1:c.1412T>C NP_001252518.1:p.Val471Ala
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.990
ToMMo:0.990
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.989

Prediction

ClinVar

Clinical Significance
Review star [No Data.]
Show details
Links
Type Database ID Link
Gene MIM 604249 OMIM
HGNC 10469 HGNC
Ensembl ENSG00000133318 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv42827587 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
0.012 anemia Meanwhile, individuals with the EMR1 rs373533 GT, EMR1 rs461645 CT and RTN3 rs54... BeFree 24934404 Detail
<0.001 anemia Meanwhile, individuals with the EMR1 rs373533 GT, EMR1 rs461645 CT and RTN3 rs54... BeFree 24934404 Detail
<0.001 anemia Meanwhile, individuals with the EMR1 rs373533 GT, EMR1 rs461645 CT and RTN3 rs54... BeFree 24934404 Detail
Annotation

Annotations

DescrptionSourceLinks
Meanwhile, individuals with the EMR1 rs373533 GT, EMR1 rs461645 CT and RTN3 rs542998 (additive C) ge... DisGeNET Detail
Meanwhile, individuals with the EMR1 rs373533 GT, EMR1 rs461645 CT and RTN3 rs542998 (additive C) ge... DisGeNET Detail
Meanwhile, individuals with the EMR1 rs373533 GT, EMR1 rs461645 CT and RTN3 rs542998 (additive C) ge... 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
hg19
Position
chr11:63,487,386-63,487,386
Variant Type
snv
Reference Allele
T
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1209
Mean of sample read depth (HGVD)
58.98
Standard deviation of sample read depth (HGVD)
28.53
Number of reference allele (HGVD)
23
Number of alternative allele (HGVD)
2390
Allele Frequency (HGVD)
0.9904682967260672
Gene Symbol (HGVD)
RTN3
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))
rs542998
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.9902
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16594
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16758
East Asian Chromosome Counts (ExAC)
8654
East Asian Allele Counts (ExAC)
8555
East Asian Heterozygous Counts (ExAC)
97
East Asian Homozygous Counts (ExAC)
4229
East Asian Allele Frequency (ExAC)
0.9885602033741623
Chromosome Counts in All Race (ExAC)
121404
Allele Counts in All Race (ExAC)
96343
Heterozygous Counts in All Race (ExAC)
17895
Homozygous Counts in All Race (ExAC)
39224
Allele Frequency in All Race (ExAC)
0.7935735231129123
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