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
  • See Evidence submitted by expert panel for details.

Variant: NM_001126049.1(KLLN):c.-792C>T

CA287473

127663 (ClinVar)

Gene: KLLN
Condition: PTEN hamartoma tumor syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: aa743dc5-7454-4c3d-8c57-501fefb597f1

HGVS expressions

NM_001126049.1:c.-792C>T
NM_001126049.1(KLLN):c.-792C>T
NC_000010.11:g.87863279G>A
CM000672.2:g.87863279G>A
NC_000010.10:g.89623036G>A
CM000672.1:g.89623036G>A
NC_000010.9:g.89613016G>A
NG_007466.2:g.4842G>A
NG_033079.1:g.5159C>T
ENST00000371953.7:c.-1191G>A
ENST00000445946.3:c.-792C>T

Uncertain Significance

Met criteria codes 1
BS1_Supporting
Not Met criteria codes 21
PS1 PS3 PS4 PS2 BP4 BP2 BP7 BP5 BA1 PP2 PP3 PP1 PM5 PM4 PM1 PM2 PM6 PVS1 BS2 BS3 BS4

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
PTEN VCEP
PTEN c.-1190G>A (NC_000010.10:g.89623036) 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). BS1_P: Allele frequency of 0.0009189 (0.09189%, 8/8706 alleles) in the African subpopulation of the gnomAD cohort. (PMID 27535533)
Met criteria codes
BS1_Supporting
AFR subpopulation allele frequency is ~0.00092.
Not Met criteria codes
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
PS4
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
BP4
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
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
BA1
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
PP3
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
PM5
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
PM1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM2
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
PVS1
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
BS3
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
Approved on: 2020-03-23
Published on: 2020-03-30
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