rs557364463
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1
This summary comes from the ClinGen Evidence Repository: PTEN c.802-51_802-14del (IVS7-51_IVS7-14del) meets criteria to be classified as benign for PTEN Hamartoma Tumor syndrome in an autosomal dominant manner using modified ACMG criteria (PMID 30311380). Please see a summary of the rules and criteria codes in the “PTEN ACMG Specifications Summary” document (assertion method column).BA1: Allele frequency of 0.01931 (1.931%, 2747/142,290 alleles) in the global gnomAD cohort. (PMID 27535533) LINK:https://erepo.genome.network/evrepo/ui/classification/CA338721/MONDO:0017623/003
Frequency
Consequence
NM_000314.8 splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTEN | NM_000314.8 | c.802-51_802-14del | splice_polypyrimidine_tract_variant, intron_variant | ENST00000371953.8 | |||
PTEN | NM_001304717.5 | c.1321-51_1321-14del | splice_polypyrimidine_tract_variant, intron_variant | ||||
PTEN | NM_001304718.2 | c.212-51_212-14del | splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTEN | ENST00000371953.8 | c.802-51_802-14del | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_000314.8 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0182 AC: 2758AN: 151158Hom.: 90 Cov.: 31
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00166 AC: 2244AN: 1354456Hom.: 6 AF XY: 0.00145 AC XY: 971AN XY: 670666
GnomAD4 genome ? AF: 0.0182 AC: 2757AN: 151260Hom.: 91 Cov.: 31 AF XY: 0.0173 AC XY: 1282AN XY: 73914
ClinVar
Submissions by phenotype
not specified Benign:3
Benign, criteria provided, single submitter | clinical testing | Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital | Aug 15, 2023 | - - |
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Mar 17, 2017 | - - |
Likely benign, no assertion criteria provided | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | - | - - |
Hereditary cancer-predisposing syndrome Benign:3
Benign, criteria provided, single submitter | clinical testing | Color Diagnostics, LLC DBA Color Health | Feb 20, 2020 | - - |
Benign, criteria provided, single submitter | curation | Sema4, Sema4 | Feb 03, 2022 | - - |
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 23, 2019 | This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
PTEN hamartoma tumor syndrome Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 06, 2023 | - - |
Benign, reviewed by expert panel | curation | Clingen PTEN Variant Curation Expert Panel, Clingen | Mar 23, 2020 | PTEN c.802-51_802-14del (IVS7-51_IVS7-14del) meets criteria to be classified as benign for PTEN Hamartoma Tumor syndrome in an autosomal dominant manner using modified ACMG criteria (PMID 30311380). Please see a summary of the rules and criteria codes in the "PTEN ACMG Specifications Summary" document (assertion method column). BA1: Allele frequency of 0.01931 (1.931%, 2747/142,290 alleles) in the global gnomAD cohort. (PMID 27535533) - |
not provided Benign:2
Benign, flagged submission | clinical testing | GeneDx | Mar 03, 2015 | This variant is associated with the following publications: (PMID: 11986403) - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 28, 2018 | - - |
Cowden syndrome 1 Uncertain:1
Uncertain significance, no assertion criteria provided | research | Cancer Genomic Medicine Translational Research Lab, Cleveland Clinic Genomic Medicine Institute | May 26, 2017 | - - |
Breast and/or ovarian cancer Benign:1
Benign, criteria provided, single submitter | clinical testing | CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario | May 18, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at