chr1:3682346:C>T Detail (hg38) (TP73)

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Information

Genome

Assembly	Position
hg19	chr1:3,598,910-3,598,910 View the variant detail on this assembly version.
hg38	chr1:3,682,346-3,682,346

Summary

Links

Type	Database	ID	Link
Gene	MIM	601990	OMIM
	HGNC	12003	HGNC
	Ensembl	ENSG00000078900	Ensembl
	NCBI		NCBI
	Gene Cards		Gene Cards
	OncoKB		OncoKB

Type	Database	ID	Link
Variant	TogoVar	tgv134858	TogoVar
	COSMIC
	MONDO

Disease area statistics

[No Data.]

MGeND

[No Data.]

ClinVar

Clinical significance	Last evaluated	Review status	Condition	Origin	Links
Benign	2023-04-11	criteria provided, single submitter	Ciliary dyskinesia, primary, 47, and lissencephaly	germline	Detail

CIViC

[No Data.]

DisGeNET

Score	Disease name	Description	Source	Pubmed	Links
0.002	Non-small cell lung carcinoma	This study investigated whether the functional polymorphisms in P53 pathway gene...	BeFree	21841506	Detail
0.219	Non-small cell lung carcinoma	This study investigated whether the functional polymorphisms in P53 pathway gene...	BeFree	21841506	Detail
<0.001	esophageal carcinoma	p21 rs3176352 G>C and p73 rs1801173 C>T polymorphisms are associated with ...	BeFree	24820515	Detail
0.001	Malignant neoplasm of esophagus	p21 rs3176352 G>C and p73 rs1801173 C>T polymorphisms are associated with ...	BeFree	24820515	Detail
<0.001	Esophageal Neoplasms	p21 rs3176352 G>C and p73 rs1801173 C>T polymorphisms are associated with ...	BeFree	24820515	Detail
<0.001	Squamous cell carcinoma of esophagus	p21 rs3176352 G>C and p73 rs1801173 C>T SNPs are associated with increased...	BeFree	24820515	Detail

Annotation

Descrption	Source	Links
NM_005427.4(TP73):c.-20C>T AND Ciliary dyskinesia, primary, 47, and lissencephaly	ClinVar	Detail
This study investigated whether the functional polymorphisms in P53 pathway genes, P53 Arg72Pro (rs1...	DisGeNET	Detail
This study investigated whether the functional polymorphisms in P53 pathway genes, P53 Arg72Pro (rs1...	DisGeNET	Detail
p21 rs3176352 G>C and p73 rs1801173 C>T polymorphisms are associated with an increased risk of...	DisGeNET	Detail
p21 rs3176352 G>C and p73 rs1801173 C>T polymorphisms are associated with an increased risk of...	DisGeNET	Detail
p21 rs3176352 G>C and p73 rs1801173 C>T polymorphisms are associated with an increased risk of...	DisGeNET	Detail
p21 rs3176352 G>C and p73 rs1801173 C>T SNPs are associated with increased risk of ESCC.	DisGeNET	Detail

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

Gene	Transcript ID	Chromosome	Start	Stop	Links

Gene: -
Genome: hg38
Position: chr1:3,682,346-3,682,346
Variant Type: snv
Reference Allele: C
Alternative Allele: T
Filtering Status (HGVD): PASS
# of samples (HGVD): 833
Mean of sample read depth (HGVD): 68.03
Standard deviation of sample read depth (HGVD): 33.48
Number of reference allele (HGVD): 1276
Number of alternative allele (HGVD): 390
Allele Frequency (HGVD): 0.234093637454982
Gene Symbol (HGVD): TP73
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)): rs1801173
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 0.2503
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 4194
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 16754
East Asian Chromosome Counts (ExAC): 2034
East Asian Allele Counts (ExAC): 697
East Asian Heterozygous Counts (ExAC): 543
East Asian Homozygous Counts (ExAC): 77
East Asian Allele Frequency (ExAC): 0.34267453294001965
Chromosome Counts in All Race (ExAC): 24678
Allele Counts in All Race (ExAC): 6881
Heterozygous Counts in All Race (ExAC): 5591
Homozygous Counts in All Race (ExAC): 645
Allele Frequency in All Race (ExAC): 0.2788313477591377

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