chr5:112839521:AAAGA> Detail (hg38) (APC)

Information

Genome

Assembly Position
hg19 chr5:112,175,218-112,175,222 
hg38 chr5:112,839,521-112,839,525

HGVS

Type Transcript Protein
RefSeq NM_000038.5:c.3927_3931delAAAGA NP_000029.2:p.Glu1309AspfsTer4
NM_001127511.2:c.3873_3877delAAAGA NP_001120983.2:p.Glu1291AspfsTer4
NM_001127510.2:c.3927_3931delAAAGA NP_001120982.1:p.Glu1309AspfsTer4
Summary

MGeND

Clinical significance Pathogenic
Variant entry 8
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:<0.001
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:<0.001

Prediction

ClinVar

Clinical Significance
Review star [No Data.]
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 tgv22330850 TogoVar
COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
Pathogenic 2021/05/01 malignant neoplasm of rectum germline MGS000029
(TMGS000133) 		Hitoshi Nakagama National Cancer Center Japan
Pathogenic 2021/05/01 other germline MGS000029
(TMGS000133) 		Hitoshi Nakagama National Cancer Center Japan
Pathogenic 2021/04/29 stomach germline MGS000029
(TMGS000133) 		Hitoshi Nakagama National Cancer Center Japan
Pathogenic 2021/04/29 colon, unspecified germline MGS000029
(TMGS000133) 		Hitoshi Nakagama National Cancer Center Japan
Pathogenic 2021/05/01 colon, unspecified germline MGS000029
(TMGS000133) 		Hitoshi Nakagama National Cancer Center Japan
Pathogenic 2020/03/04 other germline MGS000029
(TMGS000133) 		Hitoshi Nakagama National Cancer Center Japan
Pathogenic 2021/04/29 other germline MGS000029
(TMGS000133) 		Hitoshi Nakagama National Cancer Center Japan
Pathogenic 2020/03/04 colon, unspecified germline MGS000029
(TMGS000133) 		Hitoshi Nakagama National Cancer Center Japan
ClinVar
[No Data.]
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.777 Adenomatous Polyposis Coli NA CLINVAR Detail
0.121 Neoplastic Syndromes, Hereditary NA CLINVAR Detail
0.245 Gardner syndrome NA CLINVAR Detail
0.120 Polyposis, Adenomatous Intestinal NA CLINVAR Detail
Annotation

Annotations

DescrptionSourceLinks
NA DisGeNET Detail
NA DisGeNET Detail
NA DisGeNET Detail
NA 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
rs121913224 dbSNP
Genome
hg38
Position
chr5:112,839,521-112,839,525
Variant Type
snv
Reference Allele
AAAGA
Alternative Allele
-
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))
rs121913224
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0001
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
1
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8618
East Asian Allele Counts (ExAC)
0
East Asian Heterozygous Counts (ExAC)
0
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
0.0
Chromosome Counts in All Race (ExAC)
121054
Allele Counts in All Race (ExAC)
1
Heterozygous Counts in All Race (ExAC)
1
Homozygous Counts in All Race (ExAC)
0
Allele Frequency in All Race (ExAC)
8.260776182530111E-6
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