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NM_000314.7(PTEN):c.79+7A>G

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Interpretation:
Uncertain significance​

Review status:
reviewed by expert panel FDA Recognized Database
Submissions:
6 (Most recent: Jun 11, 2021)
Last evaluated:
Jul 25, 2018
Accession:
VCV000127692.7
Variation ID:
127692
Description:
single nucleotide variant
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NM_000314.7(PTEN):c.79+7A>G

Allele ID
133149
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
10q23.31
Genomic location
10: 87864555 (GRCh38) GRCh38 UCSC
10: 89624312 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000010.10:g.89624312A>G
NC_000010.11:g.87864555A>G
NM_000314.7:c.79+7A>G
... more HGVS
Protein change
-
Other names
IVS1+7A>G
NM_000314.6(PTEN):c.79+7A>G
Canonical SPDI
NC_000010.11:87864554:A:G
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00001
Trans-Omics for Precision Medicine (TOPMed) 0.00001
The Genome Aggregation Database (gnomAD), exomes 0.00001
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00015
Links
ClinGen: CA000580
dbSNP: rs374331677
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 2 reviewed by expert panel Jul 25, 2018 RCV000123050.8
Likely benign 2 criteria provided, multiple submitters, no conflicts Oct 11, 2019 RCV000115587.5
Uncertain significance 1 criteria provided, single submitter Sep 8, 2020 RCV000579577.4
Pathogenic 1 no assertion criteria provided May 26, 2017 RCV000515928.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
PTEN Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh38
GRCh37
1980 2221

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Jul 25, 2018)
reviewed by expert panel
Method: curation
PTEN hamartoma tumor syndrome
(Autosomal dominant inheritance)
Allele origin: germline
ClinGen PTEN Variant Curation Expert Panel
FDA Recognized Database
Accession: SCV000886856.1
Submitted: (Mar 05, 2019)
Evidence details
Publications
PubMed (1)
Other databases
https://erepo.clinicalgenome.org…
Comment:
PTEN c.79+7A>G (IVS1+7A>G) is currently classified as a variant of uncertain significance for PTEN Hamartoma Tumor syndrome in an autosomal dominant manner using modified ACMG … (more)
Likely benign
(Nov 22, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000149496.12
Submitted: (Mar 26, 2018)
Evidence details
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)
Likely benign
(Oct 11, 2019)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV001362400.1
Submitted: (Mar 06, 2020)
Evidence details
Publications
PubMed (3)
Comment:
Variant summary: PTEN c.79+7A>G alters a non-conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly … (more)
Likely benign
(Nov 12, 2020)
criteria provided, single submitter
Method: clinical testing
PTEN hamartoma tumor syndrome
Allele origin: germline
Invitae
Accession: SCV000166345.9
Submitted: (Jan 07, 2021)
Evidence details
Uncertain significance
(Sep 08, 2020)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Color Health, Inc
Accession: SCV000686306.4
Submitted: (Jun 11, 2021)
Evidence details
Comment:
This variant causes an A to G nucleotide substitution at the +7 position of intron 1 of the PTEN gene. A functional study reports no … (more)
Pathogenic
(May 26, 2017)
no assertion criteria provided
Method: research
Cowden syndrome 1
Allele origin: germline
Cancer Genomic Medicine Translational Research Lab,Cleveland Clinic Genomic Medicine Institute
Accession: SCV000579246.1
Submitted: (May 27, 2017)
Evidence details
Publications
PubMed (1)

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Characterization of cryptic splicing in germline PTEN intronic variants in Cowden syndrome. Chen HJ Human mutation 2017 PMID: 28677221
KLLN epigenotype-phenotype associations in Cowden syndrome. Nizialek EA European journal of human genetics : EJHG 2015 PMID: 25669429
Predicting PTEN mutations: an evaluation of Cowden syndrome and Bannayan-Riley-Ruvalcaba syndrome clinical features. Pilarski R Journal of medical genetics 2011 PMID: 21659347
https://erepo.clinicalgenome.org/evrepo/ui/interpretation/3acf8a70-e306-4b52-9401-648b6e0a3c99 - - - -

Text-mined citations for rs374331677...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Aug 27, 2021