chr5:112174096:C>T Detail (hg19) (APC)

Information

Genome

Assembly Position
hg19 chr5:112,174,096-112,174,096
hg38 chr5:112,838,399-112,838,399 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_001127511.2:c.2751C>T NP_001120983.2:p.Tyr917=
NM_000038.5:c.2805C>T NP_000029.2:p.Tyr935=
NM_001127510.2:c.2805C>T NP_001120982.1:p.Tyr935=
Summary

MGeND

Clinical significance Benign Likely benign
Variant entry 4
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 Benign Likely 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 tgv22330317 TogoVar
COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
Likely benign 2020/04/20 descending colon not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2021/03/19 Colorectal germline MGS000050
(TMGS000114) 		Yukihide Momozawa
Koichi Matsuda		 RIKEN
The University of Tokyo
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign Likely benign 2020-09-22 criteria provided, multiple submitters, no conflicts Hereditary cancer-predisposing syndrome germline Detail
Likely benign 2015-07-10 criteria provided, single submitter Familial multiple polyposis syndrome unknown Detail
Benign Likely benign 2023-08-15 criteria provided, multiple submitters, no conflicts not specified germline unknown Detail
Benign Likely benign 2023-10-01 criteria provided, multiple submitters, no conflicts not provided germline unknown Detail
Benign Likely benign 2024-03-15 criteria provided, multiple submitters, no conflicts familial adenomatous polyposis 1 germline unknown Detail
Likely benign 2018-01-13 criteria provided, single submitter APC-Associated Polyposis Disorders germline Detail
Benign no assertion criteria provided Carcinoma of colon unknown Detail
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
0.120 Polyposis, Adenomatous Intestinal NA CLINVAR Detail
0.777 Adenomatous Polyposis Coli We identified a mutation in the APC gene that results in a truncated protein (Y9... BeFree 16292097 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000038.6(APC):c.2805C>T (p.Tyr935=) AND Hereditary cancer-predisposing syndrome ClinVar Detail
NM_000038.6(APC):c.2805C>T (p.Tyr935=) AND Familial multiple polyposis syndrome ClinVar Detail
NM_000038.6(APC):c.2805C>T (p.Tyr935=) AND not specified ClinVar Detail
NM_000038.6(APC):c.2805C>T (p.Tyr935=) AND not provided ClinVar Detail
NM_000038.6(APC):c.2805C>T (p.Tyr935=) AND Familial adenomatous polyposis 1 ClinVar Detail
NM_000038.6(APC):c.2805C>T (p.Tyr935=) AND APC-Associated Polyposis Disorders ClinVar Detail
NM_000038.6(APC):c.2805C>T (p.Tyr935=) AND Carcinoma of colon ClinVar Detail
NA DisGeNET Detail
NA DisGeNET Detail
NA DisGeNET Detail
We identified a mutation in the APC gene that results in a truncated protein (Y935X) in the FAP prob... 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
rs137854575 dbSNP
Genome
hg19
Position
chr5:112,174,096-112,174,096
Variant Type
snv
Reference Allele
C
Alternative Allele
T
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))
rs137854575
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0002
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
3
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8614
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)
121044
Allele Counts in All Race (ExAC)
62
Heterozygous Counts in All Race (ExAC)
62
Homozygous Counts in All Race (ExAC)
0
Allele Frequency in All Race (ExAC)
5.12210435874558E-4
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