Evidence Repository
The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • Despite there being a valid 'cspec' property in the messages there's a discrepancy in message contents and CSPEC data: * Message Gene: PTEN CSPEC Genes: [ 'PTEN' ] * Message MONDOs: MONDO:0017623 CSPEC MONDO: []
  • No CSPEC computed assertion could be determined for this classification!

Variant: NM_000314.8(PTEN):c.-799G>C

CA000581

127674 (ClinVar)

Gene: PTEN
Condition: PTEN hamartoma tumor syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 400140b3-b081-46b3-8b10-03492bb903d0
Approved on: 2025-03-07
Published on: 2025-10-08

HGVS expressions

NM_000314.8:c.-799G>C
NM_000314.8(PTEN):c.-799G>C
NC_000010.11:g.87863671G>C
CM000672.2:g.87863671G>C
NC_000010.10:g.89623428G>C
CM000672.1:g.89623428G>C
NC_000010.9:g.89613408G>C
NG_007466.2:g.5234G>C
NG_033079.1:g.4767C>G
ENST00000700029.2:c.-799G>C
ENST00000710265.1:c.-799G>C
ENST00000706954.1:c.-16-783G>C
ENST00000706955.1:c.-799G>C
ENST00000688158.1:c.-799G>C
ENST00000688308.1:c.-17+558G>C
ENST00000693560.1:c.-279G>C
ENST00000371953.8:c.-799G>C
ENST00000371953.7:c.-799G>C
ENST00000610634.1:c.-901G>C
NM_000314.5:c.-798G>C
NM_000314.6:c.-798G>C
NM_001304717.2:c.-279G>C
NM_001304718.1:c.-1503G>C
NM_000314.7:c.-798G>C
NM_001304717.5:c.-279G>C
NM_001304718.2:c.-1503G>C
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Uncertain Significance

Not Met criteria codes 3
PM2 BS3 BS1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen PTEN Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for PTEN Version 3.1.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
PTEN VCEP
PTEN c.-798G>C (NC_000010.10:g.89623428G>C) is currently classified as a variant of uncertain significance 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). No criteria currently apply to this variant.
Not Met criteria codes
PM2
gnomAD v2 (10-89623428-G-C): Absent gnomAD v4 (10-87863671-G-C): Multiple alleles present in 3 different subpopulations (ASJ, RMI, NFE), one of which meets PM2_P criterion (NFE (2/222616 alleles): 0.000008984 [0.0008984%] < 0.00002 [0.002%]); however, this variant is covered in <50% of individuals in gnomAD v4.1.0 exomes. Allele frequency estimates may not be reliable.
BS3
Variant demonstrated normal nuclear-protein binding, luciferase activity, and PTEN mRNA levels
BS1
gnomAD v2 (10-89623428-G-C): Absent gnomAD v4 (10-87863671-G-C): Both FAF exome (0.000215%) and FAF total (0.000149%) values fall below the BS1_Supporting, minimum value (0.00043%). This variant is covered in <50% of individuals in gnomAD v4.1.0 exomes. Allele frequency estimates may not be reliable.
Curation History
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