chr5:112177331:G>A Detail (hg19) (APC)

Information

Genome

Assembly Position
hg19 chr5:112,177,331-112,177,331
hg38 chr5:112,841,634-112,841,634 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_000038.5:c.6040G>A NP_000029.2:p.Val2014Ile
NM_001127510.2:c.6040G>A NP_001120982.1:p.Val2014Ile
NM_001127511.2:c.5986G>A NP_001120983.2:p.Val1996Ile
Summary

MGeND

Clinical significance Benign Uncertain significance not provided
Variant entry 49
GWAS entry
Disease area statistics Show details

Frequency

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

Prediction

ClinVar

Clinical Significance Uncertain significance
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 tgv22331776 TogoVar
COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
not provided fundus of stomach not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
not provided caecum not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
not provided head of pancreas not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
not provided ill-defined sites within the digestive system not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
not provided bronchus or lung, unspecified not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
Uncertain significance 2021/03/19 control germline MGS000047
(TMGS000111) 		Yukihide Momozawa
Koichi Matsuda		 RIKEN
The University of Tokyo
Uncertain significance 2021/03/19 Colorectal germline MGS000050
(TMGS000114) 		Yukihide Momozawa
Koichi Matsuda		 RIKEN
The University of Tokyo
Benign 2021/03/19 pancreatic germline MGS000051
(TMGS000115) 		Yukihide Momozawa
Koichi Matsuda		 RIKEN
The University of Tokyo
Benign Centenarian germline MGS000068
(TMGS000140) 		Kenjiro Kosaki Keio University
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Uncertain significance 2017-02-20 criteria provided, single submitter not specified germline Detail
Uncertain significance 2021-06-08 criteria provided, single submitter Hereditary cancer-predisposing syndrome germline Detail
Uncertain significance 2023-01-30 criteria provided, multiple submitters, no conflicts familial adenomatous polyposis 1 unknown Detail
Uncertain significance 2022-11-28 criteria provided, single submitter familial adenomatous polyposis 1 germline Detail
CIViC
[No Data.]
DisGeNET
[No Data.]
Annotation

Annotations

DescrptionSourceLinks
NM_000038.6(APC):c.6040G>A (p.Val2014Ile) AND not specified ClinVar Detail
NM_000038.6(APC):c.6040G>A (p.Val2014Ile) AND Hereditary cancer-predisposing syndrome ClinVar Detail
NM_000038.6(APC):c.6040G>A (p.Val2014Ile) AND Familial adenomatous polyposis 1 ClinVar Detail
NM_000038.6(APC):c.6040G>A (p.Val2014Ile) AND Familial adenomatous polyposis 1 ClinVar 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
rs143313902 dbSNP
Genome
hg19
Position
chr5:112,177,331-112,177,331
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
138.65
Standard deviation of sample read depth (HGVD)
61.90
Number of reference allele (HGVD)
2418
Number of alternative allele (HGVD)
2
Allele Frequency (HGVD)
8.264462809917355E-4
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))
rs143313902
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0004
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
6
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)
1
East Asian Heterozygous Counts (ExAC)
1
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
1.1576753878212549E-4
Chromosome Counts in All Race (ExAC)
120768
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)
8.280339162692104E-6
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