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

CA163550

140783 (ClinVar)

Gene: PTEN

Condition: PTEN hamartoma tumor syndrome

Inheritance Mode: Autosomal dominant inheritance

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
ENST00000706954.1:c.-17+657C>A
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

Uncertain Significance

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

Expert Panel

PTEN VCEP

Criteria Specification Information

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

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

• 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
• 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
• 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
• 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
• 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
• 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
• BS2: 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
• 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