chr2:47373492:G>A Detail (hg38) (EPCAM)

Information

Genome

Assembly Position
hg19 chr2:47,600,631-47,600,631 View the variant detail on this assembly version.
hg38 chr2:47,373,492-47,373,492

HGVS

Type Transcript Protein
RefSeq NM_002354.2:c.106G>A NP_002345.2:p.Val36Ile
Ensemble ENST00000263735.9:c.106G>A ENST00000263735.9:p.Val36Ile
ENST00000405271.5:c.190G>A ENST00000405271.5:p.Val64Ile
Summary

MGeND

Clinical significance
Variant entry
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 Benign Likely benign
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 tgv6778197 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2023-01-09 criteria provided, single submitter not provided germline Detail
Likely benign 2019-10-15 criteria provided, single submitter EPCAM-related disorder germline Detail
CIViC
[No Data.]
DisGeNET
[No Data.]
Annotation

Annotations

DescrptionSourceLinks
NM_002354.3(EPCAM):c.106G>A (p.Val36Ile) AND not provided ClinVar Detail
NM_002354.3(EPCAM):c.106G>A (p.Val36Ile) AND EPCAM-related disorder 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
rs771315207 dbSNP
Genome
hg38
Position
chr2:47,373,492-47,373,492
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
Filtering Status (HGVD)
LowQual
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
67.81
Standard deviation of sample read depth (HGVD)
29.65
Number of reference allele (HGVD)
2418
Number of alternative allele (HGVD)
2
Allele Frequency (HGVD)
8.264462809917355E-4
Gene Symbol (HGVD)
EPCAM
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))
rs771315207
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))
1
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8540
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)
118558
Allele Counts in All Race (ExAC)
27
Heterozygous Counts in All Race (ExAC)
25
Homozygous Counts in All Race (ExAC)
1
Allele Frequency in All Race (ExAC)
2.2773663523338787E-4
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