chr1:160823770:A>G Detail (hg38) (LY9)

Information

Genome

Assembly Position
hg19 chr1:160,793,560-160,793,560 View the variant detail on this assembly version.
hg38 chr1:160,823,770-160,823,770

HGVS

Type Transcript Protein
RefSeq NM_002348.3:c.1804A>G NP_002339.2:p.Met602Val
NM_001261456.1:c.1762A>G NP_001248385.1:p.Met588Val
NM_001261457.1:c.1534A>G NP_001248386.1:p.Met512Val
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 Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 600684 OMIM
HGNC 6730 HGNC
Ensembl ENSG00000122224 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv3503638 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2020-02-18 criteria provided, single submitter not provided germline 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

DescrptionSourceLinks
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

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs509749 dbSNP
Genome
hg38
Position
chr1:160,823,770-160,823,770
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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