chr5:112841059:T>A Detail (hg38) (APC)

Information

Genome

Assembly Position
hg19 chr5:112,176,756-112,176,756 View the variant detail on this assembly version.
hg38 chr5:112,841,059-112,841,059

HGVS

Type Transcript Protein
RefSeq NM_000038.5:c.5465T>A NP_000029.2:p.Val1822Asp
NM_001127511.2:c.5411T>A NP_001120983.2:p.Val1804Asp
NM_001127510.2:c.5465T>A NP_001120982.1:p.Val1822Asp
Summary

MGeND

Clinical significance Benign
Variant entry 1
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.915
ToMMo:0.906
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.902

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 611731 OMIM
HGNC 583 HGNC
Ensembl ENSG00000134982 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv22331529 TogoVar
COSMIC COSM3760871 COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
Benign Centenarian germline MGS000068
(TMGS000140) 		Kenjiro Kosaki Keio University
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2023-02-26 reviewed by expert panel familial adenomatous polyposis 1 germline Detail
Benign 2023-11-30 criteria provided, multiple submitters, no conflicts not provided germline Detail
Benign 2016-03-16 criteria provided, multiple submitters, no conflicts not specified germline unknown Detail
other no assertion criteria provided Familial colorectal cancer unknown Detail
Benign 2015-03-27 criteria provided, multiple submitters, no conflicts Hereditary cancer-predisposing syndrome germline Detail
Benign 2018-03-06 criteria provided, single submitter APC-Associated Polyposis Disorders germline Detail
Benign no assertion criteria provided Familial multiple polyposis syndrome unknown Detail
not provided no assertion provided familial adenomatous polyposis 1 unknown Detail
Benign 2024-02-05 criteria provided, single submitter Classic or attenuated familial adenomatous polyposis germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.201 Malignant neoplasm of ovary We studied nine single nucleotide polymorphisms (SNPs) located in CTNNB1 (β-cate... BeFree 24078348 Detail
0.280 Malignant neoplasm of ovary We studied nine single nucleotide polymorphisms (SNPs) located in CTNNB1 (β-cate... BeFree 24078348 Detail
<0.001 ovarian carcinoma We studied nine single nucleotide polymorphisms (SNPs) located in CTNNB1 (β-cate... BeFree 24078348 Detail
0.003 Malignant neoplasm of ovary We studied nine single nucleotide polymorphisms (SNPs) located in CTNNB1 (β-cate... BeFree 24078348 Detail
0.002 ovarian carcinoma We studied nine single nucleotide polymorphisms (SNPs) located in CTNNB1 (β-cate... BeFree 24078348 Detail
0.082 ovarian carcinoma We studied nine single nucleotide polymorphisms (SNPs) located in CTNNB1 (β-cate... BeFree 24078348 Detail
0.076 colorectal carcinoma This study seeks to determine whether there is any association of the I1307K, E1... BeFree 18343606 Detail
0.240 colorectal cancer This study seeks to determine whether there is any association of the I1307K, E1... BeFree 18343606 Detail
0.191 adenoma APC Asp1822Val and Gly2502Ser polymorphisms and risk of colorectal cancer and ad... BeFree 15824157 Detail
0.240 colorectal cancer APC Asp1822Val and Gly2502Ser polymorphisms and risk of colorectal cancer and ad... BeFree 15824157 Detail
0.076 colorectal carcinoma APC Asp1822Val and Gly2502Ser polymorphisms and risk of colorectal cancer and ad... BeFree 15824157 Detail
0.240 colorectal cancer The D1822V APC polymorphism interacts with fat, calcium, and fiber intakes in mo... BeFree 17556698 Detail
0.076 colorectal carcinoma The D1822V APC polymorphism interacts with fat, calcium, and fiber intakes in mo... BeFree 17556698 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000038.6(APC):c.5465T>A (p.Val1822Asp) AND Familial adenomatous polyposis 1 ClinVar Detail
NM_000038.6(APC):c.5465T>A (p.Val1822Asp) AND not provided ClinVar Detail
NM_000038.6(APC):c.5465T>A (p.Val1822Asp) AND not specified ClinVar Detail
NM_000038.6(APC):c.5465T>A (p.Val1822Asp) AND Familial colorectal cancer ClinVar Detail
NM_000038.6(APC):c.5465T>A (p.Val1822Asp) AND Hereditary cancer-predisposing syndrome ClinVar Detail
NM_000038.6(APC):c.5465T>A (p.Val1822Asp) AND APC-Associated Polyposis Disorders ClinVar Detail
NM_000038.6(APC):c.5465T>A (p.Val1822Asp) AND Familial multiple polyposis syndrome ClinVar Detail
NM_000038.6(APC):c.5465T>A (p.Val1822Asp) AND Familial adenomatous polyposis 1 ClinVar Detail
NM_000038.6(APC):c.5465T>A (p.Val1822Asp) AND Classic or attenuated familial adenomatous polyposis ClinVar Detail
We studied nine single nucleotide polymorphisms (SNPs) located in CTNNB1 (β-catenin) [rs4533622, rs2... DisGeNET Detail
We studied nine single nucleotide polymorphisms (SNPs) located in CTNNB1 (β-catenin) [rs4533622, rs2... DisGeNET Detail
We studied nine single nucleotide polymorphisms (SNPs) located in CTNNB1 (β-catenin) [rs4533622, rs2... DisGeNET Detail
We studied nine single nucleotide polymorphisms (SNPs) located in CTNNB1 (β-catenin) [rs4533622, rs2... DisGeNET Detail
We studied nine single nucleotide polymorphisms (SNPs) located in CTNNB1 (β-catenin) [rs4533622, rs2... DisGeNET Detail
We studied nine single nucleotide polymorphisms (SNPs) located in CTNNB1 (β-catenin) [rs4533622, rs2... DisGeNET Detail
This study seeks to determine whether there is any association of the I1307K, E1317Q and D1822V vari... DisGeNET Detail
This study seeks to determine whether there is any association of the I1307K, E1317Q and D1822V vari... DisGeNET Detail
APC Asp1822Val and Gly2502Ser polymorphisms and risk of colorectal cancer and adenoma. DisGeNET Detail
APC Asp1822Val and Gly2502Ser polymorphisms and risk of colorectal cancer and adenoma. DisGeNET Detail
APC Asp1822Val and Gly2502Ser polymorphisms and risk of colorectal cancer and adenoma. DisGeNET Detail
The D1822V APC polymorphism interacts with fat, calcium, and fiber intakes in modulating the risk of... DisGeNET Detail
The D1822V APC polymorphism interacts with fat, calcium, and fiber intakes in modulating the risk of... 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
rs459552 dbSNP
Genome
hg38
Position
chr5:112,841,059-112,841,059
Variant Type
snv
Reference Allele
T
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
64.04
Standard deviation of sample read depth (HGVD)
30.10
Number of reference allele (HGVD)
206
Number of alternative allele (HGVD)
2214
Allele Frequency (HGVD)
0.9148760330578513
Gene Symbol (HGVD)
APC
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))
rs459552
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.9056
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
15178
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8638
East Asian Allele Counts (ExAC)
7790
East Asian Heterozygous Counts (ExAC)
776
East Asian Homozygous Counts (ExAC)
3507
East Asian Allele Frequency (ExAC)
0.9018291271127575
Chromosome Counts in All Race (ExAC)
120944
Allele Counts in All Race (ExAC)
96526
Heterozygous Counts in All Race (ExAC)
18782
Homozygous Counts in All Race (ExAC)
38872
Allele Frequency in All Race (ExAC)
0.7981049080566213
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