chr2:47803438:C>T Detail (hg38) (MSH6, FBXO11)

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

Information

Genome

Assembly	Position
hg19	chr2:48,030,577-48,030,577 View the variant detail on this assembly version.
hg38	chr2:47,803,438-47,803,438

HGVS

FBXO11
MSH6

Type	Transcript	Protein
RefSeq
Ensemble	ENST00000405808.5:c.169+4757G>A

Type	Transcript	Protein
RefSeq	NM_000179.2:c.3191C>T	NP_000170.1:p.Ala1064Val
	NM_001281492.1:c.2801C>T	NP_001268421.1:p.Ala934Val
Ensemble	ENST00000234420.11:c.3191C>T	ENST00000234420.11:p.Ala1064Val
	ENST00000411819.2:c.2894C>T	ENST00000411819.2:p.Ala965Val
	ENST00000420813.6:c.2894C>T	ENST00000420813.6:p.Ala965Val
	ENST00000455383.6:c.2894C>T	ENST00000455383.6:p.Ala965Val
	ENST00000540021.6:c.2801C>T	ENST00000540021.6:p.Ala934Val
	ENST00000652107.1:c.2894C>T	ENST00000652107.1:p.Ala965Val
	ENST00000673637.1:c.2894C>T	ENST00000673637.1:p.Ala965Val
	ENST00000700000.1:c.1625C>T	ENST00000700000.1:p.Ala542Val
	ENST00000700002.1:c.3197C>T	ENST00000700002.1:p.Ala1066Val
	ENST00000700004.2:c.3173-2180C>T

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	COSM6949532	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	COSM6949532	COSMIC
	MONDO

Disease area statistics

[No Data.]

MGeND

[No Data.]

ClinVar

Clinical significance	Last evaluated	Review status	Condition	Origin	Links
Uncertain significance	2024-01-18	criteria provided, multiple submitters, no conflicts	Hereditary cancer-predisposing syndrome	germline	Detail
Likely benign	2023-11-17	criteria provided, single submitter	Hereditary nonpolyposis colorectal neoplasms	germline	Detail
Uncertain significance	2017-09-26	criteria provided, multiple submitters, no conflicts	not provided	germline	Detail
Uncertain significance	2023-12-01	criteria provided, single submitter	Lynch syndrome	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.3191C>T (p.Ala1064Val) AND Hereditary cancer-predisposing syndrome	ClinVar	Detail
NM_000179.3(MSH6):c.3191C>T (p.Ala1064Val) AND Hereditary nonpolyposis colorectal neoplasms	ClinVar	Detail
NM_000179.3(MSH6):c.3191C>T (p.Ala1064Val) AND not provided	ClinVar	Detail
NM_000179.3(MSH6):c.3191C>T (p.Ala1064Val) AND Lynch syndrome	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: rs369042519 dbSNP
Genome: hg38
Position: chr2:47,803,438-47,803,438
Variant Type: snv
Reference Allele: C
Alternative Allele: T
East Asian Chromosome Counts (ExAC): 8648
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): 121312
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): 1.6486415193880244E-5

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