chr12:57968715:C>G Detail (hg19) (KIF5A)

Information

Genome

Assembly Position
hg19 chr12:57,968,715-57,968,715
hg38 chr12:57,574,932-57,574,932 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_004984.2:c.1717-152C>G
Ensemble ENST00000455537.7:c.1717-152C>G
ENST00000674619.1:c.1717-152C>G
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:0.801
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:[No Data.]

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 602821 OMIM
HGNC 6323 HGNC
Ensembl ENSG00000155980 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv46076577 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2018-06-14 criteria provided, single submitter not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.254 rheumatoid arthritis [Common variants at CD40 and other loci confer risk of rheumatoid arthritis.] GAD 18794853 Detail
0.254 rheumatoid arthritis Common variants at CD40 and other loci confer risk of rheumatoid arthritis. GWASCAT 18794853 Detail
0.254 rheumatoid arthritis Novel rheumatoid arthritis susceptibility locus at 22q12 identified in an extend... GWASCAT 24449572 Detail
0.345 rheumatoid arthritis Eight markers (ie, rs1160542 (AFF3), rs1678542 (KIF5A), rs2476601 (PTPN22), rs30... BeFree 20498205 Detail
0.311 rheumatoid arthritis Eight markers (ie, rs1160542 (AFF3), rs1678542 (KIF5A), rs2476601 (PTPN22), rs30... BeFree 20498205 Detail
0.277 rheumatoid arthritis Eight markers (ie, rs1160542 (AFF3), rs1678542 (KIF5A), rs2476601 (PTPN22), rs30... BeFree 20498205 Detail
0.317 rheumatoid arthritis Eight markers (ie, rs1160542 (AFF3), rs1678542 (KIF5A), rs2476601 (PTPN22), rs30... BeFree 20498205 Detail
0.524 rheumatoid arthritis Eight markers (ie, rs1160542 (AFF3), rs1678542 (KIF5A), rs2476601 (PTPN22), rs30... BeFree 20498205 Detail
0.254 rheumatoid arthritis Eight markers (ie, rs1160542 (AFF3), rs1678542 (KIF5A), rs2476601 (PTPN22), rs30... BeFree 20498205 Detail
0.129 rheumatoid arthritis Eight markers (ie, rs1160542 (AFF3), rs1678542 (KIF5A), rs2476601 (PTPN22), rs30... BeFree 20498205 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_004984.4(KIF5A):c.1717-152C>G AND not provided ClinVar Detail
[Common variants at CD40 and other loci confer risk of rheumatoid arthritis.] DisGeNET Detail
Common variants at CD40 and other loci confer risk of rheumatoid arthritis. DisGeNET Detail
Novel rheumatoid arthritis susceptibility locus at 22q12 identified in an extended UK genome-wide as... DisGeNET Detail
Eight markers (ie, rs1160542 (AFF3), rs1678542 (KIF5A), rs2476601 (PTPN22), rs3087243 (CTLA4), rs481... DisGeNET Detail
Eight markers (ie, rs1160542 (AFF3), rs1678542 (KIF5A), rs2476601 (PTPN22), rs3087243 (CTLA4), rs481... DisGeNET Detail
Eight markers (ie, rs1160542 (AFF3), rs1678542 (KIF5A), rs2476601 (PTPN22), rs3087243 (CTLA4), rs481... DisGeNET Detail
Eight markers (ie, rs1160542 (AFF3), rs1678542 (KIF5A), rs2476601 (PTPN22), rs3087243 (CTLA4), rs481... DisGeNET Detail
Eight markers (ie, rs1160542 (AFF3), rs1678542 (KIF5A), rs2476601 (PTPN22), rs3087243 (CTLA4), rs481... DisGeNET Detail
Eight markers (ie, rs1160542 (AFF3), rs1678542 (KIF5A), rs2476601 (PTPN22), rs3087243 (CTLA4), rs481... DisGeNET Detail
Eight markers (ie, rs1160542 (AFF3), rs1678542 (KIF5A), rs2476601 (PTPN22), rs3087243 (CTLA4), rs481... DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs1678542 dbSNP
Genome
hg19
Position
chr12:57,968,715-57,968,715
Variant Type
snv
Reference Allele
C
Alternative Allele
G
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))
rs1678542
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.8011
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
13427
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
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