chr2:48027540:C>T Detail (hg19) (MSH6, FBXO11)

Information

Genome

Assembly Position
hg19 chr2:48,027,540-48,027,540
hg38 chr2:47,800,401-47,800,401 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq
Ensemble ENST00000405808.5:c.169+7794G>A
Type Transcript Protein
RefSeq NM_000179.2:c.2418C>T NP_000170.1:p.Ser806=
NM_001281492.1:c.2028C>T NP_001268421.1:p.Ser676=
Ensemble ENST00000234420.11:c.2418C>T ENST00000234420.11:p.Ser806=
Summary

MGeND

Clinical significance Likely benign
Variant entry 4
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:<0.001
ToMMo:[No Data.]
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 tgv6795058 TogoVar
COSMIC COSM1318901 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 tgv6795058 TogoVar
COSMIC COSM1318901 COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
Likely benign 2019/11/26 corpus uteri, unspecified germline MGS000029
(TMGS000133) 		Hitoshi Nakagama National Cancer Center Japan
Likely benign 2019/11/26 breast, unspecified germline MGS000029
(TMGS000133) 		Hitoshi Nakagama National Cancer Center Japan
Likely benign 2020/04/20 caecum not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
Likely benign 2020/04/20 descending colon not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Likely benign 2021-05-29 criteria provided, multiple submitters, no conflicts Hereditary cancer-predisposing syndrome germline Detail
Likely benign 2019-09-03 criteria provided, single submitter not specified germline Detail
Conflicting interpretations of pathogenicity 2020-05-27 criteria provided, conflicting interpretations not provided germline unknown Detail
Likely benign 2024-01-16 criteria provided, single submitter Hereditary nonpolyposis colorectal neoplasms germline Detail
Likely benign 2024-02-05 criteria provided, single submitter Lynch syndrome germline Detail
CIViC
[No Data.]
DisGeNET
[No Data.]
Annotation

Annotations

DescrptionSourceLinks
NM_000179.3(MSH6):c.2418C>T (p.Ser806=) AND Hereditary cancer-predisposing syndrome ClinVar Detail
NM_000179.3(MSH6):c.2418C>T (p.Ser806=) AND not specified ClinVar Detail
NM_000179.3(MSH6):c.2418C>T (p.Ser806=) AND not provided ClinVar Detail
NM_000179.3(MSH6):c.2418C>T (p.Ser806=) AND Hereditary nonpolyposis colorectal neoplasms ClinVar Detail
NM_000179.3(MSH6):c.2418C>T (p.Ser806=) AND Lynch syndrome 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
rs770992427 dbSNP
Genome
hg19
Position
chr2:48,027,540-48,027,540
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
Filtering Status (HGVD)
LowQual
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
181.31
Standard deviation of sample read depth (HGVD)
81.23
Number of reference allele (HGVD)
2419
Number of alternative allele (HGVD)
1
Allele Frequency (HGVD)
4.1322314049586776E-4
Gene Symbol (HGVD)
MSH6
East Asian Chromosome Counts (ExAC)
8614
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)
120960
Allele Counts in All Race (ExAC)
2
Heterozygous Counts in All Race (ExAC)
2
Homozygous Counts in All Race (ExAC)
0
Allele Frequency in All Race (ExAC)
1.6534391534391536E-5
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