chr16:68833344:G>A Detail (hg38) (CDH1)

Information

Genome

Assembly Position
hg19 chr16:68,867,247-68,867,247 View the variant detail on this assembly version.
hg38 chr16:68,833,344-68,833,344

HGVS

Type Transcript Protein
RefSeq NM_001317184.1:c.2494G>A NP_001304113.1:p.Val832Met
NM_001317186.1:c.2494G>A NP_001304115.1:p.Val832Met
NM_004360.4:c.2494G>A NP_004351.1:p.Val832Met
Summary

MGeND

Clinical significance Benign other
Variant entry 2
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.006
ToMMo:0.005
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.003

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 192090 OMIM
HGNC 1748 HGNC
Ensembl ENSG00000039068 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv55928235 TogoVar
COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
other 2017/12/14 Undifferentiated endometrial sarcoma germline MGS000017
(TMGS000052) 		Kohei Miyazono Tokyo University
Benign Centenarian germline MGS000068
(TMGS000140) 		Kenjiro Kosaki Keio University
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Conflicting interpretations of pathogenicity 2024-01-21 criteria provided, conflicting interpretations Hereditary diffuse gastric adenocarcinoma germline Detail
Conflicting interpretations of pathogenicity 2021-03-11 criteria provided, conflicting interpretations Hereditary cancer-predisposing syndrome germline Detail
Benign 2023-08-15 criteria provided, multiple submitters, no conflicts not specified germline Detail
Likely pathogenic 2014-06-01 no assertion criteria provided Neoplasm of stomach germline Detail
Conflicting interpretations of pathogenicity 2019-12-27 criteria provided, conflicting interpretations not provided germline unknown Detail
Uncertain significance 2019-05-01 criteria provided, single submitter hereditary breast ovarian cancer syndrome germline Detail
Benign 2023-08-10 reviewed by expert panel CDH1-related diffuse gastric and lobular breast cancer syndrome germline Detail
Benign 2020-01-21 criteria provided, single submitter CDH1-related disorder germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.389 hereditary diffuse gastric cancer NA CLINVAR Detail
0.123 Neoplastic Syndromes, Hereditary NA CLINVAR Detail
0.389 hereditary diffuse gastric cancer E-cadherin gene variants in gastric cancer families whose probands are diagnosed... UNIPROT 12216071 Detail
0.339 Stomach Neoplasms NA CLINVAR Detail
Annotation

Annotations

DescrptionSourceLinks
NM_004360.5(CDH1):c.2494G>A (p.Val832Met) AND Hereditary diffuse gastric adenocarcinoma ClinVar Detail
NM_004360.5(CDH1):c.2494G>A (p.Val832Met) AND Hereditary cancer-predisposing syndrome ClinVar Detail
NM_004360.5(CDH1):c.2494G>A (p.Val832Met) AND not specified ClinVar Detail
NM_004360.5(CDH1):c.2494G>A (p.Val832Met) AND Neoplasm of stomach ClinVar Detail
NM_004360.5(CDH1):c.2494G>A (p.Val832Met) AND not provided ClinVar Detail
NM_004360.5(CDH1):c.2494G>A (p.Val832Met) AND Hereditary breast ovarian cancer syndrome ClinVar Detail
NM_004360.5(CDH1):c.2494G>A (p.Val832Met) AND CDH1-related diffuse gastric and lobular breast cancer... ClinVar Detail
NM_004360.5(CDH1):c.2494G>A (p.Val832Met) AND CDH1-related disorder ClinVar Detail
NA DisGeNET Detail
NA DisGeNET Detail
E-cadherin gene variants in gastric cancer families whose probands are diagnosed with diffuse gastri... 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
rs35572355 dbSNP
Genome
hg38
Position
chr16:68,833,344-68,833,344
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1200
Mean of sample read depth (HGVD)
49.51
Standard deviation of sample read depth (HGVD)
24.44
Number of reference allele (HGVD)
2386
Number of alternative allele (HGVD)
14
Allele Frequency (HGVD)
0.005833333333333334
Gene Symbol (HGVD)
CDH1
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))
rs35572355
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.005
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
84
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8654
East Asian Allele Counts (ExAC)
22
East Asian Heterozygous Counts (ExAC)
22
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
0.002542177027963947
Chromosome Counts in All Race (ExAC)
121412
Allele Counts in All Race (ExAC)
29
Heterozygous Counts in All Race (ExAC)
29
Homozygous Counts in All Race (ExAC)
0
Allele Frequency in All Race (ExAC)
2.3885612624781734E-4
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