chr10:121577821:A>G Detail (hg38) (FGFR2)

Information

Genome

Assembly Position
hg19 chr10:123,337,335-123,337,335 View the variant detail on this assembly version.
hg38 chr10:121,577,821-121,577,821

HGVS

Type Transcript Protein
RefSeq NM_001144916.1:c.109+15888T>C
NM_001144918.1:c.109+15888T>C
NM_001144915.1:c.110-13242T>C
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:0.566
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 176943 OMIM
HGNC 3689 HGNC
Ensembl ENSG00000066468 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv40910499 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2024-01-29 criteria provided, single submitter FGFR2-related craniosynostosis germline Detail
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
0.230 Malignant neoplasm of breast Large-scale genotyping identifies 41 new loci associated with breast cancer risk... GWASCAT 23535729 Detail
0.230 Malignant neoplasm of breast A multistage genome-wide association study in breast cancer identifies two new r... GWASCAT 19330030 Detail
0.230 Malignant neoplasm of breast Genome-wide association study identifies five new breast cancer susceptibility l... GWASCAT 20453838 Detail
<0.001 Carcinoma of male breast Five SNPs showed a statistically significant association with male breast cancer... BeFree 21949660 Detail
<0.001 Malignant neoplasm of male breast Five SNPs showed a statistically significant association with male breast cancer... BeFree 21949660 Detail
0.031 breast carcinoma Five SNPs associated with breast cancer risk predominantly among ER-positive tum... BeFree 22965832 Detail
0.080 breast carcinoma Five SNPs associated with breast cancer risk predominantly among ER-positive tum... BeFree 22965832 Detail
0.240 Malignant neoplasm of breast Five SNPs associated with breast cancer risk predominantly among ER-positive tum... BeFree 22965832 Detail
0.230 Malignant neoplasm of breast Five SNPs associated with breast cancer risk predominantly among ER-positive tum... BeFree 22965832 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000141.5(FGFR2):c.110-12117T>C AND FGFR2-related craniosynostosis ClinVar 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
Two SNPs showed significantly stronger associations for ILC than LCIS (rs2981579/10q26/FGFR2, P-het ... DisGeNET Detail
Large-scale genotyping identifies 41 new loci associated with breast cancer risk. DisGeNET Detail
A multistage genome-wide association study in breast cancer identifies two new risk alleles at 1p11.... DisGeNET Detail
Genome-wide association study identifies five new breast cancer susceptibility loci. DisGeNET Detail
Five SNPs showed a statistically significant association with male breast cancer: rs13387042 (2q35) ... DisGeNET Detail
Five SNPs showed a statistically significant association with male breast cancer: rs13387042 (2q35) ... DisGeNET Detail
Five SNPs associated with breast cancer risk predominantly among ER-positive tumors (rs2981582/FGFR2... DisGeNET Detail
Five SNPs associated with breast cancer risk predominantly among ER-positive tumors (rs2981582/FGFR2... DisGeNET Detail
Five SNPs associated with breast cancer risk predominantly among ER-positive tumors (rs2981582/FGFR2... DisGeNET Detail
Five SNPs associated with breast cancer risk predominantly among ER-positive tumors (rs2981582/FGFR2... DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs2981579 dbSNP
Genome
hg38
Position
chr10:121,577,821-121,577,821
Variant Type
snv
Reference Allele
A
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))
rs2981579
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.5658
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
9482
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
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