chr2:48025953:A>C Detail (hg19) (MSH6, FBXO11)

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Summary
Information
Links
Disease area statistics
MGeND
ClinVar
CIViC
DisGeNET
Annotation
Genome browser

Information

Genome

Assembly	Position
hg19	chr2:48,025,953-48,025,953
hg38	chr2:47,798,814-47,798,814 View the variant detail on this assembly version.

HGVS

FBXO11
MSH6

Type	Transcript	Protein
RefSeq
Ensemble	ENST00000405808.5:c.170-9374T>G

Type	Transcript	Protein
RefSeq	NM_000179.2:c.831A>C	NP_000170.1:p.Glu277Asp
	NM_001281492.1:c.441A>C	NP_001268421.1:p.Glu147Asp
Ensemble	ENST00000234420.11:c.831A>C	ENST00000234420.11:p.Glu277Asp
	ENST00000411819.2:c.534A>C	ENST00000411819.2:p.Glu178Asp
	ENST00000420813.6:c.534A>C	ENST00000420813.6:p.Glu178Asp
	ENST00000455383.6:c.534A>C	ENST00000455383.6:p.Glu178Asp
	ENST00000540021.6:c.441A>C	ENST00000540021.6:p.Glu147Asp
	ENST00000652107.1:c.534A>C	ENST00000652107.1:p.Glu178Asp
	ENST00000673637.1:c.534A>C	ENST00000673637.1:p.Glu178Asp
	ENST00000700000.1:c.831A>C	ENST00000700000.1:p.Glu277Asp
	ENST00000700002.1:c.837A>C	ENST00000700002.1:p.Glu279Asp
	ENST00000700004.2:c.831A>C	ENST00000700004.2:p.Glu277Asp

Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics	Show details

Frequency

JP	HGVD:[No Data.]
	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

FBXO11
MSH6

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
	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
	COSMIC
	MONDO

Disease area statistics

[No Data.]

MGeND

[No Data.]

ClinVar

Clinical significance	Last evaluated	Review status	Condition	Origin	Links
Conflicting interpretations of pathogenicity	2023-03-15	criteria provided, conflicting interpretations	Hereditary cancer-predisposing syndrome	germline	Detail
Benign	2024-01-11	criteria provided, single submitter	Hereditary nonpolyposis colorectal neoplasms	germline	Detail
Uncertain significance	2023-09-06	criteria provided, multiple submitters, no conflicts	not provided	germline unknown	Detail
Uncertain significance	2023-03-29	criteria provided, multiple submitters, no conflicts	Lynch syndrome 5	unknown	Detail
Uncertain significance	2018-04-30	criteria provided, single submitter	not specified	germline	Detail
Uncertain significance	2022-03-31	criteria provided, single submitter	Lynch syndrome 5,endometrial carcinoma,Mismatch repair cancer syndrome 3	unknown	Detail
Uncertain significance	2022-03-31	criteria provided, single submitter	Lynch syndrome 5,endometrial carcinoma,Mismatch repair cancer syndrome 3	unknown	Detail
Uncertain significance	2022-03-31	criteria provided, single submitter	Lynch syndrome 5,endometrial carcinoma,Mismatch repair cancer syndrome 3	unknown	Detail
Uncertain significance	2023-10-19	criteria provided, single submitter	endometrial carcinoma	unknown	Detail
Uncertain significance	2023-09-17	criteria provided, single submitter	Lynch syndrome	germline	Detail
Uncertain significance	2023-08-23	criteria provided, single submitter	MSH6-related disorder	germline	Detail

CIViC

[No Data.]

DisGeNET

Score	Disease name	Description	Source	Pubmed	Links
0.085	Malignant neoplasm of breast	Using data/samples collected from the first 752 Caucasians and 141 African-Ameri...	BeFree	18701435	Detail
0.008	breast carcinoma	Using data/samples collected from the first 752 Caucasians and 141 African-Ameri...	BeFree	18701435	Detail
0.015	Malignant neoplasm of breast	Using data/samples collected from the first 752 Caucasians and 141 African-Ameri...	BeFree	18701435	Detail
0.011	breast carcinoma	Using data/samples collected from the first 752 Caucasians and 141 African-Ameri...	BeFree	18701435	Detail
0.002	breast carcinoma	Using data/samples collected from the first 752 Caucasians and 141 African-Ameri...	BeFree	18701435	Detail
0.009	Malignant neoplasm of breast	Using data/samples collected from the first 752 Caucasians and 141 African-Ameri...	BeFree	18701435	Detail
0.019	Malignant neoplasm of breast	Using data/samples collected from the first 752 Caucasians and 141 African-Ameri...	BeFree	18701435	Detail
0.001	breast carcinoma	Using data/samples collected from the first 752 Caucasians and 141 African-Ameri...	BeFree	18701435	Detail
0.004	breast carcinoma	Using data/samples collected from the first 752 Caucasians and 141 African-Ameri...	BeFree	18701435	Detail
0.018	breast carcinoma	Using data/samples collected from the first 752 Caucasians and 141 African-Ameri...	BeFree	18701435	Detail
0.023	Malignant neoplasm of breast	Using data/samples collected from the first 752 Caucasians and 141 African-Ameri...	BeFree	18701435	Detail
0.013	Malignant neoplasm of breast	Using data/samples collected from the first 752 Caucasians and 141 African-Ameri...	BeFree	18701435	Detail
0.002	breast carcinoma	Using data/samples collected from the first 752 Caucasians and 141 African-Ameri...	BeFree	18701435	Detail
0.098	Malignant neoplasm of breast	Using data/samples collected from the first 752 Caucasians and 141 African-Ameri...	BeFree	18701435	Detail

Annotation

Annotations

Descrption	Source	Links
NM_000179.3(MSH6):c.831A>C (p.Glu277Asp) AND Hereditary cancer-predisposing syndrome	ClinVar	Detail
NM_000179.3(MSH6):c.831A>C (p.Glu277Asp) AND Hereditary nonpolyposis colorectal neoplasms	ClinVar	Detail
NM_000179.3(MSH6):c.831A>C (p.Glu277Asp) AND not provided	ClinVar	Detail
NM_000179.3(MSH6):c.831A>C (p.Glu277Asp) AND Lynch syndrome 5	ClinVar	Detail
NM_000179.3(MSH6):c.831A>C (p.Glu277Asp) AND not specified	ClinVar	Detail
NM_000179.3(MSH6):c.831A>C (p.Glu277Asp) AND multiple conditions	ClinVar	Detail
NM_000179.3(MSH6):c.831A>C (p.Glu277Asp) AND multiple conditions	ClinVar	Detail
NM_000179.3(MSH6):c.831A>C (p.Glu277Asp) AND multiple conditions	ClinVar	Detail
NM_000179.3(MSH6):c.831A>C (p.Glu277Asp) AND Endometrial carcinoma	ClinVar	Detail
NM_000179.3(MSH6):c.831A>C (p.Glu277Asp) AND Lynch syndrome	ClinVar	Detail
NM_000179.3(MSH6):c.831A>C (p.Glu277Asp) AND MSH6-related disorder	ClinVar	Detail
Using data/samples collected from the first 752 Caucasians and 141 African-Americans in an ongoing c...	DisGeNET	Detail
Using data/samples collected from the first 752 Caucasians and 141 African-Americans in an ongoing c...	DisGeNET	Detail
Using data/samples collected from the first 752 Caucasians and 141 African-Americans in an ongoing c...	DisGeNET	Detail
Using data/samples collected from the first 752 Caucasians and 141 African-Americans in an ongoing c...	DisGeNET	Detail
Using data/samples collected from the first 752 Caucasians and 141 African-Americans in an ongoing c...	DisGeNET	Detail
Using data/samples collected from the first 752 Caucasians and 141 African-Americans in an ongoing c...	DisGeNET	Detail
Using data/samples collected from the first 752 Caucasians and 141 African-Americans in an ongoing c...	DisGeNET	Detail
Using data/samples collected from the first 752 Caucasians and 141 African-Americans in an ongoing c...	DisGeNET	Detail
Using data/samples collected from the first 752 Caucasians and 141 African-Americans in an ongoing c...	DisGeNET	Detail
Using data/samples collected from the first 752 Caucasians and 141 African-Americans in an ongoing c...	DisGeNET	Detail
Using data/samples collected from the first 752 Caucasians and 141 African-Americans in an ongoing c...	DisGeNET	Detail
Using data/samples collected from the first 752 Caucasians and 141 African-Americans in an ongoing c...	DisGeNET	Detail
Using data/samples collected from the first 752 Caucasians and 141 African-Americans in an ongoing c...	DisGeNET	Detail
Using data/samples collected from the first 752 Caucasians and 141 African-Americans in an ongoing c...	DisGeNET	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: rs374486449 dbSNP
Genome: hg19
Position: chr2:48,025,953-48,025,953
Variant Type: snv
Reference Allele: A
Alternative Allele: C
East Asian Chromosome Counts (ExAC): 8642
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): 121138
Allele Counts in All Race (ExAC): 4
Heterozygous Counts in All Race (ExAC): 4
Homozygous Counts in All Race (ExAC): 0
Allele Frequency in All Race (ExAC): 3.302019184731463E-5

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