chr1:202187176:G>A Detail (hg19) (LGR6)

Information

Genome

Assembly Position
hg19 chr1:202,187,176-202,187,176
hg38 chr1:202,218,048-202,218,048 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_001017403.1:c.213-7375G>A
NM_021636.2:c.57-7375G>A
NM_001017404.1:c.83+3811G>A
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:0.195
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:[No Data.]

Prediction

ClinVar

Clinical Significance
Review star [No Data.]
Show details
Links
Type Database ID Link
Gene MIM 606653 OMIM
HGNC 19719 HGNC
Ensembl ENSG00000133067 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv4445026 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 Lobular carcinoma in situ of breast Two SNPs showed significantly stronger associations for ILC than LCIS (rs2981579... BeFree 24743323 Detail
<0.001 Non-infiltrating lobular carcinoma Two SNPs showed significantly stronger associations for ILC than LCIS (rs2981579... BeFree 24743323 Detail
<0.001 Lobular carcinoma in situ of breast Two SNPs showed significantly stronger associations for ILC than LCIS (rs2981579... BeFree 24743323 Detail
<0.001 Non-infiltrating lobular carcinoma Two SNPs showed significantly stronger associations for ILC than LCIS (rs2981579... BeFree 24743323 Detail
<0.001 Lobular carcinoma in situ of breast Two SNPs showed significantly stronger associations for ILC than LCIS (rs2981579... BeFree 24743323 Detail
<0.001 Non-infiltrating lobular carcinoma Two SNPs showed significantly stronger associations for ILC than LCIS (rs2981579... BeFree 24743323 Detail
0.121 Malignant neoplasm of breast SNPs at four loci, 1q32.1 (MDM4, P = 2.1 × 10(-12) and LGR6, P = 1.4 × 10(-8)), ... GWASCAT 23535733 Detail
Annotation

Annotations

DescrptionSourceLinks
Two SNPs showed significantly stronger associations for ILC than LCIS (rs2981579/10q26/FGFR2, P-het ... DisGeNET Detail
Two SNPs showed significantly stronger associations for ILC than LCIS (rs2981579/10q26/FGFR2, P-het ... DisGeNET Detail
Two SNPs showed significantly stronger associations for ILC than LCIS (rs2981579/10q26/FGFR2, P-het ... DisGeNET Detail
Two SNPs showed significantly stronger associations for ILC than LCIS (rs2981579/10q26/FGFR2, P-het ... DisGeNET Detail
Two SNPs showed significantly stronger associations for ILC than LCIS (rs2981579/10q26/FGFR2, P-het ... DisGeNET Detail
Two SNPs showed significantly stronger associations for ILC than LCIS (rs2981579/10q26/FGFR2, P-het ... DisGeNET Detail
SNPs at four loci, 1q32.1 (MDM4, P = 2.1 × 10(-12) and LGR6, P = 1.4 × 10(-8)), 2p24.1 (P = 4.6 × 10... DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs6678914 dbSNP
Genome
hg19
Position
chr1:202,187,176-202,187,176
Variant Type
snv
Reference Allele
G
Alternative Allele
A
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))
rs6678914
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.1947
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
3264
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
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