chr16:68812144:A>G Detail (hg38) (CDH1)

Information

Genome

Assembly Position
hg19 chr16:68,846,047-68,846,047 View the variant detail on this assembly version.
hg38 chr16:68,812,144-68,812,144

HGVS

Type Transcript Protein
RefSeq NM_001317184.1:c.1018A>G NP_001304113.1:p.Thr340Ala
NM_001317186.1:c.1018A>G NP_001304115.1:p.Thr340Ala
NM_004360.4:c.1018A>G NP_004351.1:p.Thr340Ala
Summary

MGeND

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

Frequency

JP HGVD:0.003
ToMMo:0.003
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.004

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 tgv55926777 TogoVar
COSMIC COSM19821 COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
other 2018/02/08 esophageal squamous carcinoma 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
Benign Likely benign 2024-02-01 criteria provided, multiple submitters, no conflicts Hereditary diffuse gastric adenocarcinoma germline unknown Detail
Benign Likely benign 2021-02-13 criteria provided, multiple submitters, no conflicts Hereditary cancer-predisposing syndrome germline Detail
Benign 2019-02-25 criteria provided, single submitter not specified germline Detail
Uncertain significance 2017-11-29 no assertion criteria provided gastric adenocarcinoma germline Detail
Benign Likely benign 2020-11-30 criteria provided, multiple submitters, no conflicts not provided germline unknown Detail
Likely benign 2021-04-23 criteria provided, single submitter Breast and/or ovarian cancer germline Detail
Benign 2023-08-08 reviewed by expert panel CDH1-related diffuse gastric and lobular breast cancer syndrome germline Detail
Likely benign 2019-04-12 criteria provided, single submitter CDH1-related disorder germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.008 colorectal carcinoma The E-cadherin gene (CDH1) variants T340A and L599V in gastric and colorectal ca... BeFree 10896919 Detail
0.389 hereditary diffuse gastric cancer NA CLINVAR Detail
0.123 Neoplastic Syndromes, Hereditary NA CLINVAR Detail
0.171 colorectal cancer The E-cadherin gene (CDH1) variants T340A and L599V in gastric and colorectal ca... BeFree 10896919 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_004360.5(CDH1):c.1018A>G (p.Thr340Ala) AND Hereditary diffuse gastric adenocarcinoma ClinVar Detail
NM_004360.5(CDH1):c.1018A>G (p.Thr340Ala) AND Hereditary cancer-predisposing syndrome ClinVar Detail
NM_004360.5(CDH1):c.1018A>G (p.Thr340Ala) AND not specified ClinVar Detail
NM_004360.5(CDH1):c.1018A>G (p.Thr340Ala) AND Gastric adenocarcinoma ClinVar Detail
NM_004360.5(CDH1):c.1018A>G (p.Thr340Ala) AND not provided ClinVar Detail
NM_004360.5(CDH1):c.1018A>G (p.Thr340Ala) AND Breast and/or ovarian cancer ClinVar Detail
NM_004360.5(CDH1):c.1018A>G (p.Thr340Ala) AND CDH1-related diffuse gastric and lobular breast cancer... ClinVar Detail
NM_004360.5(CDH1):c.1018A>G (p.Thr340Ala) AND CDH1-related disorder ClinVar Detail
The E-cadherin gene (CDH1) variants T340A and L599V in gastric and colorectal cancer patients in Kor... DisGeNET Detail
NA DisGeNET Detail
NA DisGeNET Detail
The E-cadherin gene (CDH1) variants T340A and L599V in gastric and colorectal cancer patients in Kor... 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
rs116093741 dbSNP
Genome
hg38
Position
chr16:68,812,144-68,812,144
Variant Type
snv
Reference Allele
A
Alternative Allele
G
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1003
Mean of sample read depth (HGVD)
26.35
Standard deviation of sample read depth (HGVD)
17.97
Number of reference allele (HGVD)
2000
Number of alternative allele (HGVD)
6
Allele Frequency (HGVD)
0.0029910269192422734
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))
rs116093741
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0029
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
49
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)
31
East Asian Heterozygous Counts (ExAC)
31
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
0.003582158539403744
Chromosome Counts in All Race (ExAC)
121412
Allele Counts in All Race (ExAC)
32
Heterozygous Counts in All Race (ExAC)
32
Homozygous Counts in All Race (ExAC)
0
Allele Frequency in All Race (ExAC)
2.6356538068724676E-4
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