chr5:83353158:T>G Detail (hg38) (XRCC4)

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Information

Genome

Assembly	Position
hg19	chr5:82,648,977-82,648,977 View the variant detail on this assembly version.
hg38	chr5:83,353,158-83,353,158

Summary

Links

Type	Database	ID	Link
Gene	MIM	194363	OMIM
	HGNC	12831	HGNC
	Ensembl	ENSG00000152422	Ensembl
	NCBI		NCBI
	Gene Cards		Gene Cards
	OncoKB		OncoKB

Type	Database	ID	Link
Variant	TogoVar	tgv21729254	TogoVar
	COSMIC
	MONDO

Disease area statistics

[No Data.]

MGeND

[No Data.]

ClinVar

Clinical significance	Last evaluated	Review status	Condition	Origin	Links
Benign	2024-01-31	criteria provided, multiple submitters, no conflicts	not provided	germline	Detail
Benign	2021-12-05	criteria provided, single submitter	Short stature, microcephaly, and endocrine dysfunction	germline	Detail

CIViC

[No Data.]

DisGeNET

Score	Disease name	Description	Source	Pubmed	Links
0.003	Lymphoma, Follicular	The following genotypes in combination with hair dye use before 1980 were associ...	BeFree	25178586	Detail
0.008	Lymphoma, Follicular	The following genotypes in combination with hair dye use before 1980 were associ...	BeFree	25178586	Detail
0.017	Malignant neoplasm of breast	Genotypes in XRCC4 were associated with BC risk, with ORs of 1.67 (95 % CI 1.01-...	BeFree	24062231	Detail
0.003	Lymphoma, Follicular	The following genotypes in combination with hair dye use before 1980 were associ...	BeFree	25178586	Detail
0.003	Lymphoma, Follicular	The following genotypes in combination with hair dye use before 1980 were associ...	BeFree	25178586	Detail
0.003	breast carcinoma	Genotypes in XRCC4 were associated with BC risk, with ORs of 1.67 (95 % CI 1.01-...	BeFree	24062231	Detail
0.003	Lymphoma, Follicular	The following genotypes in combination with hair dye use before 1980 were associ...	BeFree	25178586	Detail
0.003	Lymphoma, Follicular	The following genotypes in combination with hair dye use before 1980 were associ...	BeFree	25178586	Detail
0.003	Lymphoma, Follicular	The following genotypes in combination with hair dye use before 1980 were associ...	BeFree	25178586	Detail

Annotation

Descrption	Source	Links
NM_003401.5(XRCC4):c.921T>G (p.Ser307=) AND not provided	ClinVar	Detail
NM_003401.5(XRCC4):c.921T>G (p.Ser307=) AND Short stature, microcephaly, and endocrine dysfunction	ClinVar	Detail
The following genotypes in combination with hair dye use before 1980 were associated with FL risk: B...	DisGeNET	Detail
The following genotypes in combination with hair dye use before 1980 were associated with FL risk: B...	DisGeNET	Detail
Genotypes in XRCC4 were associated with BC risk, with ORs of 1.67 (95 % CI 1.01-2.76) for the combin...	DisGeNET	Detail
The following genotypes in combination with hair dye use before 1980 were associated with FL risk: B...	DisGeNET	Detail
The following genotypes in combination with hair dye use before 1980 were associated with FL risk: B...	DisGeNET	Detail
Genotypes in XRCC4 were associated with BC risk, with ORs of 1.67 (95 % CI 1.01-2.76) for the combin...	DisGeNET	Detail
The following genotypes in combination with hair dye use before 1980 were associated with FL risk: B...	DisGeNET	Detail
The following genotypes in combination with hair dye use before 1980 were associated with FL risk: B...	DisGeNET	Detail
The following genotypes in combination with hair dye use before 1980 were associated with FL risk: B...	DisGeNET	Detail

Gene	Transcript ID	Exon Number	Chromosome	Start	Stop	Type	Amino Mutation	Transcript Position	Links

Gene	Transcript ID	Chromosome	Start	Stop	Links

Gene: -
dbSNP: rs1056503 dbSNP
Genome: hg38
Position: chr5:83,353,158-83,353,158
Variant Type: snv
Reference Allele: T
Alternative Allele: G
Filtering Status (HGVD): PASS
# of samples (HGVD): 1208
Mean of sample read depth (HGVD): 75.77
Standard deviation of sample read depth (HGVD): 42.67
Number of reference allele (HGVD): 760
Number of alternative allele (HGVD): 1656
Allele Frequency (HGVD): 0.6854304635761589
Gene Symbol (HGVD): XRCC4
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)): rs1056503
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 0.6911
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 11583
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 16760
East Asian Chromosome Counts (ExAC): 8644
East Asian Allele Counts (ExAC): 6228
East Asian Heterozygous Counts (ExAC): 1698
East Asian Homozygous Counts (ExAC): 2265
East Asian Allele Frequency (ExAC): 0.7204997686256362
Chromosome Counts in All Race (ExAC): 120824
Allele Counts in All Race (ExAC): 27776
Heterozygous Counts in All Race (ExAC): 17303
Homozygous Counts in All Race (ExAC): 5236
Allele Frequency in All Race (ExAC): 0.22988810170164867

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