chr1:160793560:A>G Detail (hg19) (LY9)
Information
Genome
Assembly | Position |
---|---|
hg19 | chr1:160,793,560-160,793,560 |
hg38 | chr1:160,823,770-160,823,770 View the variant detail on this assembly version. |
HGVS
Type | Transcript | Protein |
---|---|---|
RefSeq | NM_002348.3:c.1804A>G | NP_002339.2:p.Met602Val |
NM_001261457.1:c.1534A>G | NP_001248386.1:p.Met512Val | |
NM_001261456.1:c.1762A>G | NP_001248385.1:p.Met588Val |
Summary
MGeND
Clinical significance | |
Variant entry | |
GWAS entry | |
Disease area statistics | Show details |
Frequency
JP | HGVD:0.755 |
ToMMo:0.735 | |
NCBN:[No Data.] | |
NCBN(Hondo):[No Data.] | |
NCBN(Ryukyu):[No Data.] | |
East asia | ExAC:0.730 |
Prediction
ClinVar
Clinical Significance |
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Review star | ![]() |
Show details |
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
---|---|---|---|---|---|
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2020-02-18 | criteria provided, single submitter | not provided |
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Detail |
CIViC
[No Data.]
DisGeNET
Score | Disease name | Description | Source | Pubmed | Links |
---|---|---|---|---|---|
0.121 | rheumatoid arthritis | A characteristic single-nucleotide polymorphism (SNP) in each of 9 genetic facto... | BeFree | 19714582 | Detail |
0.125 | rheumatoid arthritis | A characteristic single-nucleotide polymorphism (SNP) in each of 9 genetic facto... | BeFree | 19714582 | Detail |
<0.001 | rheumatoid arthritis | A characteristic single-nucleotide polymorphism (SNP) in each of 9 genetic facto... | BeFree | 19714582 | Detail |
0.003 | rheumatoid arthritis | A characteristic single-nucleotide polymorphism (SNP) in each of 9 genetic facto... | BeFree | 19714582 | Detail |
Annotation
Annotations
Descrption | Source | Links |
---|---|---|
NM_002348.4(LY9):c.1804A>G (p.Met602Val) AND not provided | ClinVar | Detail |
A characteristic single-nucleotide polymorphism (SNP) in each of 9 genetic factors, ITGAM (rs1143679... | DisGeNET | Detail |
A characteristic single-nucleotide polymorphism (SNP) in each of 9 genetic factors, ITGAM (rs1143679... | DisGeNET | Detail |
A characteristic single-nucleotide polymorphism (SNP) in each of 9 genetic factors, ITGAM (rs1143679... | DisGeNET | Detail |
A characteristic single-nucleotide polymorphism (SNP) in each of 9 genetic factors, ITGAM (rs1143679... | DisGeNET | Detail |
Overlapped Transcript Coordinates
Gene | Transcript ID | Exon Number | Chromosome | Start | Stop | Type | Amino Mutation | Transcript Position | Links |
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Overlapped Transcript
Gene | Transcript ID | Chromosome | Start | Stop | Links |
---|
- Gene
- -
- dbSNP
- rs509749 dbSNP
- Genome
- hg19
- Position
- chr1:160,793,560-160,793,560
- Variant Type
- snv
- Reference Allele
- A
- Alternative Allele
- G
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1210
- Mean of sample read depth (HGVD)
- 117.78
- Standard deviation of sample read depth (HGVD)
- 56.16
- Number of reference allele (HGVD)
- 593
- Number of alternative allele (HGVD)
- 1827
- Allele Frequency (HGVD)
- 0.7549586776859504
- Gene Symbol (HGVD)
- LY9
- 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))
- rs509749
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.7351
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 12321
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8646
- East Asian Allele Counts (ExAC)
- 6315
- East Asian Heterozygous Counts (ExAC)
- 1767
- East Asian Homozygous Counts (ExAC)
- 2274
- East Asian Allele Frequency (ExAC)
- 0.7303955586398334
- Chromosome Counts in All Race (ExAC)
- 121172
- Allele Counts in All Race (ExAC)
- 65293
- Heterozygous Counts in All Race (ExAC)
- 27673
- Homozygous Counts in All Race (ExAC)
- 18810
- Allele Frequency in All Race (ExAC)
- 0.5388456078962136
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