chr2:47803696:CTTA> Detail (hg38) (MSH6, FBXO11)

Information

Genome

Assembly Position
hg19 chr2:48,030,835-48,030,838 
hg38 chr2:47,803,696-47,803,699

HGVS

Type Transcript Protein
RefSeq
Ensemble ENST00000405808.5:c.169+4496_169+4499delTAAG
Type Transcript Protein
RefSeq NM_000179.2:c.3438+11_3438+14delCTTA
NM_001281492.1:c.3048+11_3048+14delCTTA
Ensemble ENST00000234420.11:c.3438+11_3438+14delCTTA
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:0.002

Prediction

ClinVar

Clinical Significance Benign Likely benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 607871 OMIM
HGNC 13590 HGNC
Ensembl ENSG00000138081 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv6795969 TogoVar
COSMIC
MONDO
Type Database ID Link
Gene MIM 600678 OMIM
HGNC 7329 HGNC
Ensembl ENSG00000116062 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv6795969 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Uncertain significance no assertion criteria provided Carcinoma of colon unknown Detail
Benign Likely benign 2021-06-10 criteria provided, multiple submitters, no conflicts Hereditary cancer-predisposing syndrome germline Detail
Likely benign 2016-09-28 criteria provided, single submitter Lynch syndrome 5 unknown Detail
Benign Likely benign 2021-06-11 criteria provided, multiple submitters, no conflicts not provided germline Detail
Benign 2024-02-01 criteria provided, single submitter Hereditary nonpolyposis colorectal neoplasms germline Detail
Likely benign 2023-08-15 criteria provided, multiple submitters, no conflicts not specified germline Detail
Likely benign 2023-01-05 criteria provided, single submitter Breast and/or ovarian cancer germline Detail
CIViC
[No Data.]
DisGeNET
[No Data.]
Annotation

Annotations

DescrptionSourceLinks
NM_000179.3(MSH6):c.3438+11_3438+14del AND Carcinoma of colon ClinVar Detail
NM_000179.3(MSH6):c.3438+11_3438+14del AND Hereditary cancer-predisposing syndrome ClinVar Detail
NM_000179.3(MSH6):c.3438+11_3438+14del AND Lynch syndrome 5 ClinVar Detail
NM_000179.3(MSH6):c.3438+11_3438+14del AND not provided ClinVar Detail
NM_000179.3(MSH6):c.3438+11_3438+14del AND Hereditary nonpolyposis colorectal neoplasms ClinVar Detail
NM_000179.3(MSH6):c.3438+11_3438+14del AND not specified ClinVar Detail
NM_000179.3(MSH6):c.3438+11_3438+14del AND Breast and/or ovarian cancer ClinVar Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs377746844 dbSNP
Genome
hg38
Position
chr2:47,803,696-47,803,699
Variant Type
snv
Reference Allele
CTTA
Alternative Allele
-
Filtering Status (HGVD)
PASS
Filtering Status (HGVD)
LowQual
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
105.71
Standard deviation of sample read depth (HGVD)
47.73
Number of reference allele (HGVD)
2419
Number of alternative allele (HGVD)
1
Allele Frequency (HGVD)
4.1322314049586776E-4
Gene Symbol (HGVD)
MSH6
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))
rs377746844
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)
8650
East Asian Allele Counts (ExAC)
18
East Asian Heterozygous Counts (ExAC)
18
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
0.0020809248554913293
Chromosome Counts in All Race (ExAC)
120966
Allele Counts in All Race (ExAC)
27
Heterozygous Counts in All Race (ExAC)
27
Homozygous Counts in All Race (ExAC)
0
Allele Frequency in All Race (ExAC)
2.232032141262834E-4
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