chr17:48274291:T>G Detail (hg19) (COL1A1, LOC126862586)

Information

Genome

Assembly Position
hg19 chr17:48,274,291-48,274,291
hg38 chr17:50,196,930-50,196,930 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_000088.3:c.804+80A>C
Ensemble ENST00000225964.10:c.804+80A>C
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:0.605
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 120150 OMIM
HGNC 2197 HGNC
Ensembl ENSG00000108821 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv58047587 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
<0.001 breast carcinoma We genotyped 17 germline SNPs (FGFR2-rs2981582, FGFR2-rs3750817, TNRC9-rs3803662... BeFree 21791674 Detail
0.017 breast carcinoma Ten SNPs (rs2075555 in COL1A1, rs12652447 in FBXL17, rs10941679 in 5p12/MRPS30, ... BeFree 24528085 Detail
0.026 Malignant neoplasm of breast Ten SNPs (rs2075555 in COL1A1, rs12652447 in FBXL17, rs10941679 in 5p12/MRPS30, ... BeFree 24528085 Detail
0.132 Malignant neoplasm of breast We genotyped 17 germline SNPs (FGFR2-rs2981582, FGFR2-rs3750817, TNRC9-rs3803662... BeFree 21791674 Detail
0.001 breast carcinoma We genotyped 17 germline SNPs (FGFR2-rs2981582, FGFR2-rs3750817, TNRC9-rs3803662... BeFree 21791674 Detail
0.001 Malignant neoplasm of breast We genotyped 17 germline SNPs (FGFR2-rs2981582, FGFR2-rs3750817, TNRC9-rs3803662... BeFree 21791674 Detail
0.003 breast carcinoma We genotyped 17 germline SNPs (FGFR2-rs2981582, FGFR2-rs3750817, TNRC9-rs3803662... BeFree 21791674 Detail
0.123 Malignant neoplasm of breast We genotyped 17 germline SNPs (FGFR2-rs2981582, FGFR2-rs3750817, TNRC9-rs3803662... BeFree 21791674 Detail
0.123 Malignant neoplasm of breast The top SNP associations in GEE models for each trait were as follows: breast ca... GWASCAT 17903305 Detail
0.123 Malignant neoplasm of breast [The top SNP associations in GEE models for each trait were as follows: breast c... GAD 17903305 Detail
0.162 Malignant neoplasm of breast Three SNPs (LSP1-rs3817198, COL1A1-rs2075555, and RNF146-rs2180341) did not show... BeFree 21791674 Detail
0.003 Malignant neoplasm of prostate The top SNP associations in GEE models for each trait were as follows: breast ca... BeFree 17903305 Detail
0.123 Malignant neoplasm of breast Three SNPs (LSP1-rs3817198, COL1A1-rs2075555, and RNF146-rs2180341) did not show... BeFree 21791674 Detail
0.004 breast carcinoma Three SNPs (LSP1-rs3817198, COL1A1-rs2075555, and RNF146-rs2180341) did not show... BeFree 21791674 Detail
<0.001 breast carcinoma Three SNPs (LSP1-rs3817198, COL1A1-rs2075555, and RNF146-rs2180341) did not show... BeFree 21791674 Detail
<0.001 Severe myopia The frequency of GGC/GGC diplotype constructed by the three SNPs (rs2075555, rs2... BeFree 17557158 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000088.4(COL1A1):c.804+80A>C AND not provided ClinVar Detail
We genotyped 17 germline SNPs (FGFR2-rs2981582, FGFR2-rs3750817, TNRC9-rs3803662, 2q35-rs13387042, M... DisGeNET Detail
Ten SNPs (rs2075555 in COL1A1, rs12652447 in FBXL17, rs10941679 in 5p12/MRPS30, rs11878583 in ZNF577... DisGeNET Detail
Ten SNPs (rs2075555 in COL1A1, rs12652447 in FBXL17, rs10941679 in 5p12/MRPS30, rs11878583 in ZNF577... DisGeNET Detail
We genotyped 17 germline SNPs (FGFR2-rs2981582, FGFR2-rs3750817, TNRC9-rs3803662, 2q35-rs13387042, M... DisGeNET Detail
We genotyped 17 germline SNPs (FGFR2-rs2981582, FGFR2-rs3750817, TNRC9-rs3803662, 2q35-rs13387042, M... DisGeNET Detail
We genotyped 17 germline SNPs (FGFR2-rs2981582, FGFR2-rs3750817, TNRC9-rs3803662, 2q35-rs13387042, M... DisGeNET Detail
We genotyped 17 germline SNPs (FGFR2-rs2981582, FGFR2-rs3750817, TNRC9-rs3803662, 2q35-rs13387042, M... DisGeNET Detail
We genotyped 17 germline SNPs (FGFR2-rs2981582, FGFR2-rs3750817, TNRC9-rs3803662, 2q35-rs13387042, M... DisGeNET Detail
The top SNP associations in GEE models for each trait were as follows: breast cancer, rs2075555, p =... DisGeNET Detail
[The top SNP associations in GEE models for each trait were as follows: breast cancer, rs2075555, p ... DisGeNET Detail
Three SNPs (LSP1-rs3817198, COL1A1-rs2075555, and RNF146-rs2180341) did not show association with br... DisGeNET Detail
The top SNP associations in GEE models for each trait were as follows: breast cancer, rs2075555, p =... DisGeNET Detail
Three SNPs (LSP1-rs3817198, COL1A1-rs2075555, and RNF146-rs2180341) did not show association with br... DisGeNET Detail
Three SNPs (LSP1-rs3817198, COL1A1-rs2075555, and RNF146-rs2180341) did not show association with br... DisGeNET Detail
Three SNPs (LSP1-rs3817198, COL1A1-rs2075555, and RNF146-rs2180341) did not show association with br... DisGeNET Detail
The frequency of GGC/GGC diplotype constructed by the three SNPs (rs2075555, rs2269336, rs1107946) w... DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs2075555 dbSNP
Genome
hg19
Position
chr17:48,274,291-48,274,291
Variant Type
snv
Reference Allele
T
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))
rs2075555
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.6048
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
10136
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
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