chr17:7689242:C>T Detail (hg38) (TP53, WRAP53)

Information

Genome

Assembly Position
hg19 chr17:7,592,560-7,592,560 View the variant detail on this assembly version.
hg38 chr17:7,689,242-7,689,242

HGVS

Type Transcript Protein
RefSeq NM_001143992.1:c.450C>T NP_001137464.1:p.Phe150=
NM_018081.2:c.450C>T NP_060551.2:p.Phe150=
NM_001143990.1:c.450C>T NP_001137462.1:p.Phe150=
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.258
ToMMo:0.263
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.294

Prediction

ClinVar

Clinical Significance Benign Likely benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 612661 OMIM
HGNC 25522 HGNC
Ensembl ENSG00000141499 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv56958410 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2024-01-24 criteria provided, multiple submitters, no conflicts not specified germline Detail
Likely benign 2016-06-14 criteria provided, single submitter Li-Fraumeni syndrome germline Detail
Benign 2018-01-13 criteria provided, single submitter Dyskeratosis congenita, autosomal recessive 3 germline Detail
Benign 2024-02-01 criteria provided, multiple submitters, no conflicts not provided germline Detail
Benign 2015-10-08 criteria provided, single submitter dyskeratosis congenita germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.123 Malignant neoplasm of ovary In conclusion SNPs in WRAP53 (rs2287497 and rs2287498) have stronger association... BeFree 23192612 Detail
0.085 ovarian carcinoma In conclusion SNPs in WRAP53 (rs2287497 and rs2287498) have stronger association... BeFree 23192612 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_001143992.2(WRAP53):c.450C>T (p.Phe150=) AND not specified ClinVar Detail
NM_001143992.2(WRAP53):c.450C>T (p.Phe150=) AND Li-Fraumeni syndrome ClinVar Detail
NM_001143992.2(WRAP53):c.450C>T (p.Phe150=) AND Dyskeratosis congenita, autosomal recessive 3 ClinVar Detail
NM_001143992.2(WRAP53):c.450C>T (p.Phe150=) AND not provided ClinVar Detail
NM_001143992.2(WRAP53):c.450C>T (p.Phe150=) AND Dyskeratosis congenita ClinVar Detail
In conclusion SNPs in WRAP53 (rs2287497 and rs2287498) have stronger association with an ovarian can... DisGeNET Detail
In conclusion SNPs in WRAP53 (rs2287497 and rs2287498) have stronger association with an ovarian can... 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
rs2287498 dbSNP
Genome
hg38
Position
chr17:7,689,242-7,689,242
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
262.25
Standard deviation of sample read depth (HGVD)
122.83
Number of reference allele (HGVD)
1795
Number of alternative allele (HGVD)
624
Allele Frequency (HGVD)
0.2579578338156263
Gene Symbol (HGVD)
WRAP53
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))
rs2287498
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.2629
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
4406
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8642
East Asian Allele Counts (ExAC)
2537
East Asian Heterozygous Counts (ExAC)
1751
East Asian Homozygous Counts (ExAC)
393
East Asian Allele Frequency (ExAC)
0.293566304096274
Chromosome Counts in All Race (ExAC)
121374
Allele Counts in All Race (ExAC)
16152
Heterozygous Counts in All Race (ExAC)
13132
Homozygous Counts in All Race (ExAC)
1510
Allele Frequency in All Race (ExAC)
0.13307627663255722
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