chr2:47606078:A>G Detail (hg19) (EPCAM)

Information

Genome

Assembly Position
hg19 chr2:47,606,078-47,606,078
hg38 chr2:47,378,939-47,378,939 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_002354.2:c.556-14A>G
Ensemble ENST00000405271.5:c.640-14A>G
ENST00000263735.9:c.556-14A>G
Summary

MGeND

Clinical significance Pathogenic
Variant entry 2
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 Conflicting classifications of pathogenicity
Review star
Show details
Links
Type Database ID Link
Gene MIM 185535 OMIM
HGNC 11529 HGNC
Ensembl ENSG00000119888 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv6778604 TogoVar
COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
Pathogenic 2019/09/20 malignant neoplasm of thyroid gland germline MGS000029
(TMGS000133) 		Hitoshi Nakagama National Cancer Center Japan
Pathogenic 2019/09/20 malignant neoplasm of skin, unspecified germline MGS000029
(TMGS000133) 		Hitoshi Nakagama National Cancer Center Japan
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Pathogenic Likely pathogenic 2022-08-30 criteria provided, multiple submitters, no conflicts congenital diarrhea 5 with tufting enteropathy biparental germline unknown Detail
Pathogenic 2022-05-25 criteria provided, single submitter congenital diarrhea 5 with tufting enteropathy,Lynch syndrome 8 unknown Detail
Pathogenic 2022-05-25 criteria provided, single submitter congenital diarrhea 5 with tufting enteropathy,Lynch syndrome 8 unknown Detail
Uncertain significance 2023-08-02 criteria provided, single submitter Lynch syndrome 8 germline Detail
Pathogenic 2019-01-10 criteria provided, single submitter not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.562 DIARRHEA 5, WITH TUFTING ENTEROPATHY, CONGENITAL NA CLINVAR Detail
Annotation

Annotations

DescrptionSourceLinks
NM_002354.3(EPCAM):c.556-14A>G AND Congenital diarrhea 5 with tufting enteropathy ClinVar Detail
NM_002354.3(EPCAM):c.556-14A>G AND multiple conditions ClinVar Detail
NM_002354.3(EPCAM):c.556-14A>G AND multiple conditions ClinVar Detail
NM_002354.3(EPCAM):c.556-14A>G AND Lynch syndrome 8 ClinVar Detail
NM_002354.3(EPCAM):c.556-14A>G AND not provided ClinVar Detail
NA DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs376155665 dbSNP
Genome
hg19
Position
chr2:47,606,078-47,606,078
Variant Type
snv
Reference Allele
A
Alternative Allele
G
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))
rs376155665
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))
2
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8386
East Asian Allele Counts (ExAC)
1
East Asian Heterozygous Counts (ExAC)
1
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
1.1924636298592893E-4
Chromosome Counts in All Race (ExAC)
113538
Allele Counts in All Race (ExAC)
7
Heterozygous Counts in All Race (ExAC)
7
Homozygous Counts in All Race (ExAC)
0
Allele Frequency in All Race (ExAC)
6.165336715460903E-5
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