chr17:7578115:T>C Detail (hg19) (TP53)

Information

Genome

Assembly Position
hg19 chr17:7,578,115-7,578,115
hg38 chr17:7,674,797-7,674,797 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_001126113.2:c.672+62A>G
NM_001276695.1:c.672+62A>G
NM_000546.5:c.672+62A>G
Summary

MGeND

Clinical significance Benign
Variant entry 3,633
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:0.979
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.967

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 191170 OMIM
HGNC 11998 HGNC
Ensembl ENSG00000141510 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv56957184 TogoVar
COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
Benign 2020/04/20 colon, unspecified not provided MGS000040
(TMGS000095) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 cervical part of oesophagus not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 abdominal part of oesophagus not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 upper third of oesophagus not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 middle third of oesophagus not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 lower third of oesophagus not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 oesophagus, unspecified not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 fundus of stomach not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 body of stomach not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 pyloric antrum not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 stomach, unspecified not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 duodenum not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 jejunum not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 ileum not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 small intestine, unspecified not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 caecum not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 appendix not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 transverse colon not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 descending colon not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 sigmoid colon not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 overlapping lesion of colon not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 colon, unspecified not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 malignant neoplasm of rectosigmoid junction not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 malignant neoplasm of rectum not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 anal canal not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 liver cell carcinoma not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 intrahepatic bile duct carcinoma not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 malignant neoplasm of gallbladder not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 extrahepatic bile duct not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 ampulla of vater not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 head of pancreas not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 body of pancreas not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 tail of pancreas not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 ill-defined sites within the digestive system not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 bronchus or lung, unspecified not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2018-07-02 criteria provided, multiple submitters, no conflicts not specified germline Detail
Benign 2015-03-03 criteria provided, single submitter not provided germline Detail
Benign 2022-06-18 criteria provided, single submitter Li-Fraumeni syndrome 1 germline Detail
Benign 2022-06-18 criteria provided, single submitter Hereditary cancer-predisposing syndrome germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.080 Carcinoma of lung When individuals with variant-containing genotypes were compared with homozygous... BeFree 17908995 Detail
0.027 diffuse large B-cell lymphoma The G/G genotype of the TP53 rs1625895 polymorphism was shown to be associated w... BeFree 25430047 Detail
0.002 Malignant neoplasm of lung When individuals with variant-containing genotypes were compared with homozygous... BeFree 17908995 Detail
0.160 Malignant neoplasm of lung When individuals with variant-containing genotypes were compared with homozygous... BeFree 17908995 Detail
0.014 diffuse large B-cell lymphoma The G/G genotype of the TP53 rs1625895 polymorphism was shown to be associated w... BeFree 25430047 Detail
0.002 Carcinoma of lung When individuals with variant-containing genotypes were compared with homozygous... BeFree 17908995 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000546.6(TP53):c.672+62A>G AND not specified ClinVar Detail
NM_000546.6(TP53):c.672+62A>G AND not provided ClinVar Detail
NM_000546.6(TP53):c.672+62A>G AND Li-Fraumeni syndrome 1 ClinVar Detail
NM_000546.6(TP53):c.672+62A>G AND Hereditary cancer-predisposing syndrome ClinVar Detail
When individuals with variant-containing genotypes were compared with homozygous wild-type carriers,... DisGeNET Detail
The G/G genotype of the TP53 rs1625895 polymorphism was shown to be associated with a high probabili... DisGeNET Detail
When individuals with variant-containing genotypes were compared with homozygous wild-type carriers,... DisGeNET Detail
When individuals with variant-containing genotypes were compared with homozygous wild-type carriers,... DisGeNET Detail
The G/G genotype of the TP53 rs1625895 polymorphism was shown to be associated with a high probabili... DisGeNET Detail
When individuals with variant-containing genotypes were compared with homozygous wild-type carriers,... DisGeNET Detail
Non melanoma specific model (ovarian cancer) MMMP Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs1625895 dbSNP
Genome
hg19
Position
chr17:7,578,115-7,578,115
Variant Type
snv
Reference Allele
T
Alternative Allele
C
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))
rs1625895
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.979
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16408
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
5740
East Asian Allele Counts (ExAC)
5549
East Asian Heterozygous Counts (ExAC)
186
East Asian Homozygous Counts (ExAC)
2681
East Asian Allele Frequency (ExAC)
0.9667247386759582
Chromosome Counts in All Race (ExAC)
89300
Allele Counts in All Race (ExAC)
76910
Heterozygous Counts in All Race (ExAC)
10937
Homozygous Counts in All Race (ExAC)
32986
Allele Frequency in All Race (ExAC)
0.8612541993281075
MMMP State (molecule) (MMMP)
polymorphism rs1625895
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