chr2:47476361:T>C Detail (hg38) (MSH2)

Information

Genome

Assembly Position
hg19 chr2:47,703,500-47,703,500 View the variant detail on this assembly version.
hg38 chr2:47,476,361-47,476,361

HGVS

Type Transcript Protein
RefSeq NM_000251.2:c.2006-6T>C
NM_001258281.1:c.1808-6T>C
Ensemble ENST00000233146.7:c.2006-6T>C
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.250
ToMMo:0.284
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.350

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 609309 OMIM
HGNC 7325 HGNC
Ensembl ENSG00000095002 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv6784201 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2013-09-05 reviewed by expert panel Lynch syndrome germline Detail
Benign 2014-06-24 criteria provided, multiple submitters, no conflicts not specified germline unknown Detail
Benign 2023-07-07 criteria provided, multiple submitters, no conflicts Lynch syndrome 1 germline unknown Detail
Benign 2022-01-02 criteria provided, multiple submitters, no conflicts Hereditary cancer-predisposing syndrome germline Detail
Benign 2024-02-01 criteria provided, single submitter Hereditary nonpolyposis colorectal neoplasms germline Detail
Benign 2019-11-12 criteria provided, single submitter Mismatch repair cancer syndrome 1 unknown Detail
Benign 2023-11-17 criteria provided, multiple submitters, no conflicts not provided germline Detail
Benign 2021-11-10 criteria provided, single submitter Lynch syndrome 1,Mismatch repair cancer syndrome 2,Muir-Torré syndrome unknown Detail
Benign 2021-11-10 criteria provided, single submitter Lynch syndrome 1,Mismatch repair cancer syndrome 2,Muir-Torré syndrome unknown Detail
Benign 2021-11-10 criteria provided, single submitter Lynch syndrome 1,Mismatch repair cancer syndrome 2,Muir-Torré syndrome unknown Detail
CIViC
[No Data.]
DisGeNET
[No Data.]
Annotation

Annotations

DescrptionSourceLinks
NM_000251.3(MSH2):c.2006-6T>C AND Lynch syndrome ClinVar Detail
NM_000251.3(MSH2):c.2006-6T>C AND not specified ClinVar Detail
NM_000251.3(MSH2):c.2006-6T>C AND Lynch syndrome 1 ClinVar Detail
NM_000251.3(MSH2):c.2006-6T>C AND Hereditary cancer-predisposing syndrome ClinVar Detail
NM_000251.3(MSH2):c.2006-6T>C AND Hereditary nonpolyposis colorectal neoplasms ClinVar Detail
NM_000251.3(MSH2):c.2006-6T>C AND Mismatch repair cancer syndrome 1 ClinVar Detail
NM_000251.3(MSH2):c.2006-6T>C AND not provided ClinVar Detail
NM_000251.3(MSH2):c.2006-6T>C AND multiple conditions ClinVar Detail
NM_000251.3(MSH2):c.2006-6T>C AND multiple conditions ClinVar Detail
NM_000251.3(MSH2):c.2006-6T>C AND multiple conditions ClinVar Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs2303428 dbSNP
Genome
hg38
Position
chr2:47,476,361-47,476,361
Variant Type
snv
Reference Allele
T
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1059
Mean of sample read depth (HGVD)
33.14
Standard deviation of sample read depth (HGVD)
14.38
Number of reference allele (HGVD)
1588
Number of alternative allele (HGVD)
530
Allele Frequency (HGVD)
0.2502360717658168
Gene Symbol (HGVD)
MSH2
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))
rs2303428
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.2836
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
4753
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8578
East Asian Allele Counts (ExAC)
3002
East Asian Heterozygous Counts (ExAC)
1930
East Asian Homozygous Counts (ExAC)
536
East Asian Allele Frequency (ExAC)
0.34996502681277686
Chromosome Counts in All Race (ExAC)
119492
Allele Counts in All Race (ExAC)
13796
Heterozygous Counts in All Race (ExAC)
11554
Homozygous Counts in All Race (ExAC)
1121
Allele Frequency in All Race (ExAC)
0.11545542797844208
Genome browser