chr5:112828864:G>A Detail (hg38) (APC)

Information

Genome

Assembly Position
hg19 chr5:112,164,561-112,164,561 View the variant detail on this assembly version.
hg38 chr5:112,828,864-112,828,864

HGVS

Type Transcript Protein
RefSeq NM_000038.5:c.1635G>A NP_000029.2:p.Ala545=
NM_001127511.2:c.1581G>A NP_001120983.2:p.Ala527=
NM_001127510.2:c.1635G>A NP_001120982.1:p.Ala545=
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.855
ToMMo:0.858
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.823

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 tgv22329473 TogoVar
COSMIC COSM3760868 COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
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 2016-03-18 criteria provided, multiple submitters, no conflicts Hereditary cancer-predisposing syndrome germline Detail
Benign 2018-01-13 criteria provided, single submitter APC-Associated Polyposis Disorders germline Detail
Benign 2023-02-19 reviewed by expert panel familial adenomatous polyposis 1 germline unknown Detail
Benign no assertion criteria provided Carcinoma of colon unknown Detail
Benign 2023-11-29 criteria provided, multiple submitters, no conflicts not provided 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
0.002 ovarian carcinoma Our study demonstrated significantly increased APC rs11954856 and rs351771 SNP f... 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
0.082 Malignant neoplasm of ovary Our study demonstrated significantly increased APC rs11954856 and rs351771 SNP f... 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
Annotation

Annotations

DescrptionSourceLinks
NM_000038.6(APC):c.1635G>A (p.Ala545=) AND not specified ClinVar Detail
NM_000038.6(APC):c.1635G>A (p.Ala545=) AND Familial colorectal cancer ClinVar Detail
NM_000038.6(APC):c.1635G>A (p.Ala545=) AND Hereditary cancer-predisposing syndrome ClinVar Detail
NM_000038.6(APC):c.1635G>A (p.Ala545=) AND APC-Associated Polyposis Disorders ClinVar Detail
NM_000038.6(APC):c.1635G>A (p.Ala545=) AND Familial adenomatous polyposis 1 ClinVar Detail
NM_000038.6(APC):c.1635G>A (p.Ala545=) AND Carcinoma of colon ClinVar Detail
NM_000038.6(APC):c.1635G>A (p.Ala545=) AND not provided ClinVar Detail
We studied nine single nucleotide polymorphisms (SNPs) located in CTNNB1 (β-catenin) [rs4533622, rs2... DisGeNET Detail
Our study demonstrated significantly increased APC rs11954856 and rs351771 SNP frequencies in Polish... 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
Our study demonstrated significantly increased APC rs11954856 and rs351771 SNP frequencies in Polish... 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

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
rs351771 dbSNP
Genome
hg38
Position
chr5:112,828,864-112,828,864
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1207
Mean of sample read depth (HGVD)
78.75
Standard deviation of sample read depth (HGVD)
32.98
Number of reference allele (HGVD)
350
Number of alternative allele (HGVD)
2064
Allele Frequency (HGVD)
0.8550124275062138
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))
rs351771
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.8575
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
14371
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8606
East Asian Allele Counts (ExAC)
7083
East Asian Heterozygous Counts (ExAC)
1263
East Asian Homozygous Counts (ExAC)
2910
East Asian Allele Frequency (ExAC)
0.8230304438763654
Chromosome Counts in All Race (ExAC)
121146
Allele Counts in All Race (ExAC)
78516
Heterozygous Counts in All Race (ExAC)
26680
Homozygous Counts in All Race (ExAC)
25918
Allele Frequency in All Race (ExAC)
0.6481105443019167
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