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]
Link to SEPIO compliant JSON-LD document
  • There was no gene found in the curated document received from the VCI/VCEP
  • Gene listed was thus derived from ClinVar and/or CAR

Variant: NM_001126049.1(KLLN):c.-812G>T

CA163550

140783 (ClinVar)

Gene: N/A
Condition: PTEN hamartoma tumor syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 38e83f92-035d-49b6-a143-0b4d0bb03969
Approved on: 2020-10-20
Published on: 2022-09-30

HGVS expressions

NM_001126049.1(KLLN):c.-812G>T
NC_000010.11:g.87863299C>A
CM000672.2:g.87863299C>A
NC_000010.10:g.89623056C>A
CM000672.1:g.89623056C>A
NC_000010.9:g.89613036C>A
NG_007466.2:g.4862C>A
NG_033079.1:g.5139G>T
ENST00000688308.1:c.-17+186C>A
ENST00000445946.5:c.-812G>T
ENST00000371953.7:c.-1171C>A
ENST00000445946.3:c.-812G>T
NM_001126049.1:c.-812G>T
NM_001126049.2:c.-812G>T
NM_001126049.2(KLLN):c.-812G>T

Uncertain Significance

The Expert Panel has overridden the computationally generated classification - "[unknown]"
Not Met criteria codes 26
PM1 PM4 PM5 PM3 PM2 PM6 BS3 BS1 BS4 BS2 BP7 BP5 BP3 BP4 BP1 BP2 PS1 PS3 PS2 PS4 PVS1 BA1 PP3 PP2 PP4 PP1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen PTEN Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines Version 2

PDF
Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
PTEN VCEP
PTEN c.-1170C>A, also described as c.-1171C>A (NC_000010.10:g.89623056C>A) 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
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
PM5
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
PM2
Variant AKA c.-1171C>A (Clinvar 140783) is present in gnomAD v. 3 (2/143372 alleles) which is .00001395, therefore not less than .001%
PM6
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
BS1
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
BS2
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
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
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
BP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS1
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
PS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS4
Gene Dx internal lab data: several cases picked up on panels with no helpful info, no co-occurrences, no segregation data
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
PP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP2
Promotor variant
PP4
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
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