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Variant: NM_000314.6(PTEN):c.-734G>A

CA10602385

127672 (ClinVar)

Gene: PTEN
Condition: PTEN hamartoma tumor syndrome
Inheritance Mode: Autosomal dominant inheritance
UUID: ffaaa038-c2bf-425c-b1d9-29e7adab495b
Approved on: 2023-08-04
Published on: 2023-10-19

HGVS expressions

NM_000314.6:c.-734G>A
NM_000314.6(PTEN):c.-734G>A
NC_000010.11:g.87863735G>A
CM000672.2:g.87863735G>A
NC_000010.10:g.89623492G>A
CM000672.1:g.89623492G>A
NC_000010.9:g.89613472G>A
NG_007466.2:g.5298G>A
NG_033079.1:g.4703C>T
ENST00000688158.1:c.-735G>A
ENST00000688308.1:c.-17+622G>A
ENST00000693560.1:c.-215G>A
ENST00000371953.8:c.-735G>A
ENST00000371953.7:c.-735G>A
ENST00000610634.1:c.-837G>A
NM_000314.5:c.-734G>A
NM_001304717.2:c.-215G>A
NM_001304718.1:c.-1439G>A
NM_000314.7:c.-734G>A
NM_001304717.5:c.-215G>A
NM_001304718.2:c.-1439G>A
NM_000314.8:c.-735G>A
NM_000314.8(PTEN):c.-735G>A
More

Likely Benign

Met criteria codes 1
BS1
Not Met criteria codes 25
BS2 BS4 BS3 BP3 BP2 BP4 BP1 BP7 BP5 PS1 PS2 PS4 PS3 PVS1 BA1 PP1 PP4 PP3 PP2 PM5 PM1 PM4 PM3 PM6 PM2

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 3.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
PTEN VCEP
NM_000314.8(PTEN):c.-735G>A meets criteria to be classified as likely benign for PTEN Hamartoma Tumor syndrome in an autosomal dominant manner using modified ACMG criteria (ACMG Classification Rules Specified for PTEN Variant Curation version 3.0.0). Please see a summary of the rules and criteria codes in the “PTEN ACMG Specifications Summary” document (assertion method column). BS1: To be applied for variants with filtering allele frequency (FAF) of 0.000043 up to 0.00056 (0.0043% up to 0.056%) in gnomAD. Popmax FAF in gnomAD for South Asians: 0.01758%. Per ClinGen PTEN Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for PTEN Version 3, 1 Benign Strong = Likely Benign.
Met criteria codes
BS1
Popmax filtering allele frequency in gnomAD (FAF) for South Asians: 0.01758% (BS1 cutoff: 0.0043%)
Not Met criteria codes
BS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP2
Per M. Perpich: University of Washington lab reported in ClinVar that the proband has a de novo causative mutation in PPP2R5D and mother has PTEN variant without clinical phenotype. Per J. Mester: case might count for BP5 (below), reached out to lab for clinical details.
BP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP7
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP5
Per M. Perpich: University of Washington lab reported in ClinVar that the proband has a de novo causative mutation in PPP2R5D and mother has PTEN variant without clinical phenotype. MP changed to not met since need 2 cases to meet BP5. Per J. Mester: case might count, reached out to lab for clinical details.
PS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PVS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BA1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM6
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM2
4/30,690 global gnomAD alleles, N insufficient for subpop benign criteria. MP agrees.
Curation History
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