chr2:48030669:C>T Detail (hg19) (MSH6, FBXO11)

Information

Genome

Assembly Position
hg19 chr2:48,030,669-48,030,669
hg38 chr2:47,803,530-47,803,530 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq
Ensemble ENST00000405808.5:c.169+4665G>A
Type Transcript Protein
RefSeq NM_000179.2:c.3283C>T NP_000170.1:p.Arg1095Cys
NM_001281492.1:c.2893C>T NP_001268421.1:p.Arg965Cys
Ensemble ENST00000234420.11:c.3283C>T ENST00000234420.11:p.Arg1095Cys
Summary

MGeND

Clinical significance Uncertain significance not provided
Variant entry 47
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 607871 OMIM
HGNC 13590 HGNC
Ensembl ENSG00000138081 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv6795849 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 tgv6795849 TogoVar
COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
Uncertain significance 2021/07/24 malignant neoplasm of rectum germline MGS000029
(TMGS000133) 		Hitoshi Nakagama National Cancer Center Japan
Uncertain significance 2019/05/15 pancreas, unspecified germline MGS000029
(TMGS000133) 		Hitoshi Nakagama National Cancer Center Japan
Uncertain significance 2021/03/19 control germline MGS000047
(TMGS000111) 		Yukihide Momozawa
Koichi Matsuda		 RIKEN
The University of Tokyo
Uncertain significance 2021/03/19 Colorectal germline MGS000050
(TMGS000114) 		Yukihide Momozawa
Koichi Matsuda		 RIKEN
The University of Tokyo
not provided caecum not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
not provided sigmoid colon not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
not provided ampulla of vater not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
not provided ill-defined sites within the digestive system not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
not provided bronchus or lung, unspecified not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Conflicting interpretations of pathogenicity 2022-12-07 criteria provided, conflicting interpretations Hereditary cancer-predisposing syndrome germline Detail
Likely benign 2021-06-21 criteria provided, single submitter not specified germline Detail
Uncertain significance 2024-01-11 criteria provided, multiple submitters, no conflicts Lynch syndrome germline Detail
Conflicting interpretations of pathogenicity 2023-03-29 criteria provided, conflicting interpretations Lynch syndrome 5 germline unknown Detail
Uncertain significance 2023-09-07 criteria provided, multiple submitters, no conflicts not provided germline Detail
Likely benign 2024-01-19 criteria provided, single submitter Hereditary nonpolyposis colorectal neoplasms germline Detail
Uncertain significance 2022-09-13 criteria provided, single submitter Breast and/or ovarian cancer germline Detail
Uncertain significance 2023-10-13 criteria provided, single submitter endometrial carcinoma unknown Detail
CIViC
[No Data.]
DisGeNET
[No Data.]
Annotation

Annotations

DescrptionSourceLinks
NM_000179.3(MSH6):c.3283C>T (p.Arg1095Cys) AND Hereditary cancer-predisposing syndrome ClinVar Detail
NM_000179.3(MSH6):c.3283C>T (p.Arg1095Cys) AND not specified ClinVar Detail
NM_000179.3(MSH6):c.3283C>T (p.Arg1095Cys) AND Lynch syndrome ClinVar Detail
NM_000179.3(MSH6):c.3283C>T (p.Arg1095Cys) AND Lynch syndrome 5 ClinVar Detail
NM_000179.3(MSH6):c.3283C>T (p.Arg1095Cys) AND not provided ClinVar Detail
NM_000179.3(MSH6):c.3283C>T (p.Arg1095Cys) AND Hereditary nonpolyposis colorectal neoplasms ClinVar Detail
NM_000179.3(MSH6):c.3283C>T (p.Arg1095Cys) AND Breast and/or ovarian cancer ClinVar Detail
NM_000179.3(MSH6):c.3283C>T (p.Arg1095Cys) AND Endometrial carcinoma 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
rs376243329 dbSNP
Genome
hg19
Position
chr2:48,030,669-48,030,669
Variant Type
snv
Reference Allele
C
Alternative Allele
T
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))
rs376243329
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0004
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
7
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)
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)
121374
Allele Counts in All Race (ExAC)
9
Heterozygous Counts in All Race (ExAC)
9
Homozygous Counts in All Race (ExAC)
0
Allele Frequency in All Race (ExAC)
7.415097137772504E-5
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