Variant: NM_000314.8(PTEN):c.-837C>T

CA000604

189497 (ClinVar)

Gene: PTEN

Condition: PTEN hamartoma tumor syndrome

Inheritance Mode: Autosomal dominant inheritance

UUID: 33db34fc-6e87-4071-927e-75502052d33d

HGVS expressions

NM_000314.8:c.-837C>T
NM_000314.8(PTEN):c.-837C>T
NC_000010.11:g.87863633C>T
CM000672.2:g.87863633C>T
NC_000010.10:g.89623390C>T
CM000672.1:g.89623390C>T
NC_000010.9:g.89613370C>T
NG_007466.2:g.5196C>T
NG_033079.1:g.4805G>A
ENST00000688158.1:c.-837C>T
ENST00000688308.1:c.-17+520C>T
ENST00000692337.1:c.75C>T
ENST00000693560.1:c.-317C>T
ENST00000371953.8:c.-837C>T
ENST00000371953.7:c.-837C>T
ENST00000610634.1:c.-939C>T
NM_000314.5:c.-836C>T
NM_000314.6:c.-836C>T
NM_001304717.2:c.-317C>T
NM_001304718.1:c.-1541C>T
NM_000314.7:c.-836C>T
NM_001304717.5:c.-317C>T
NM_001304718.2:c.-1541C>T

Likely Benign

• Met criteria codes: BP5 BS1_Supporting

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

Expert Panel

PTEN VCEP

Criteria Specification Information

Criteria Specification: ClinGen PTEN Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for PTEN Version 3.0.0

Evidence submitted by expert panel

PTEN VCEP

NM_000314.8(PTEN):c.-837C>T 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_P: To be applied for variants with filtering allele frequency of 0.0000043 up to 0.000043 (0.00043% up to 0.0043%) in gnomAD. Popmax FAF of this variant=0.00003249 [0.003249%] in gnomAD v3. BP5: Variant found in multiple cases with alternate molecular basis for disease. (internal laboratory contributor(s))

Met criteria codes

• BP5: Variant found in multiple cases with alternate molecular basis for disease. (internal laboratory contributor(s))
• BS1_Supporting: To be applied for variants with filtering allele frequency of 0.0000043 up to 0.000043 (0.00043% up to 0.0043%) in gnomAD. Popmax FAF of this variant=0.00003249 [0.003249%] in gnomAD v3.

Not Met criteria codes

• 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
• BP7: 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: 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
• 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
• BS2: 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
• PP1: 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: 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
• 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
• 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

Approved on: 2023-10-11

Published on: 2023-10-18