chr10:87960892:A>T Detail (hg38) (PTEN)

Information

Genome

Assembly Position
hg19 chr10:89,720,649-89,720,649 View the variant detail on this assembly version.
hg38 chr10:87,960,892-87,960,892

HGVS

Type Transcript Protein
RefSeq NM_000314.6:c.802-2A>T
NM_001304717.2:c.802-2A>T
NM_001304718.1:c.802-2A>T
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.028
ToMMo:[No Data.]
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:[No Data.]

Prediction

ClinVar

Clinical Significance Pathogenic
Review star
Show details
Links
Type Database ID Link
Gene MIM 601728 OMIM
HGNC 9588 HGNC
Ensembl ENSG00000171862 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv40102648 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Pathogenic 2023-05-23 criteria provided, single submitter Hereditary cancer-predisposing syndrome germline Detail
Pathogenic 2023-10-24 criteria provided, multiple submitters, no conflicts not provided germline Detail
Pathogenic 2023-05-10 criteria provided, single submitter Cowden syndrome 1 germline unknown Detail
Pathogenic 2017-10-18 reviewed by expert panel PTEN hamartoma tumor syndrome germline Detail
Pathogenic 2023-11-29 criteria provided, single submitter PTEN-related disorder germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.122 Neoplastic Syndromes, Hereditary NA CLINVAR Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000314.8(PTEN):c.802-2A>T AND Hereditary cancer-predisposing syndrome ClinVar Detail
NM_000314.8(PTEN):c.802-2A>T AND not provided ClinVar Detail
NM_000314.8(PTEN):c.802-2A>T AND Cowden syndrome 1 ClinVar Detail
NM_000314.8(PTEN):c.802-2A>T AND PTEN hamartoma tumor syndrome ClinVar Detail
NM_000314.8(PTEN):c.802-2A>T AND PTEN-related disorder ClinVar Detail
NA DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs587782455 dbSNP
Genome
hg38
Position
chr10:87,960,892-87,960,892
Variant Type
snv
Reference Allele
A
Alternative Allele
T
Filtering Status (HGVD)
PASS
Filtering Status (HGVD)
VQSRTrancheSNP99.00to99.90
# of samples (HGVD)
836
Mean of sample read depth (HGVD)
11.33
Standard deviation of sample read depth (HGVD)
12.86
Number of reference allele (HGVD)
1624
Number of alternative allele (HGVD)
47
Allele Frequency (HGVD)
0.028126870137642132
Gene Symbol (HGVD)
PTEN
Genome browser