This sample table of contents illustrates how a Notice of Discrepancies may be broken down into procedural defenses, income-tax issues, VAT issues, withholding-tax issues, evidentiary gaps, date anomalies, jurisprudence, and a document-submission plan.
Intro
Purpose and How to Use This Report
[redacted]
Overview of NOD Findings and Status
[redacted]
A
Procedural Defects - Raise These First
[redacted]
A-1
The NOD Bears No Date of Issuance
[redacted]
A-2
NOD Template and Response-Period Issues under RMC No. 102-2020
[redacted]
A-3
Blank or Unverified Electronic Letter of Authority Details
[redacted]
A-4
Subpoena Duces Tecum Compliance Review
[redacted]
B
Undeclared Income - SI/BI vs. ITR Reconciliation
[redacted]
B-1
What the BIR Is Alleging
[redacted]
B-2
Issues in the BIR Analysis: out-of-period invoices, billing statements, gross-vs-net comparison, and income-recognition rules
[redacted]
B-3
Documents to Gather and Arguments to Make; Reconciliation Schedule
[redacted]
C
Alleged Missing Invoices - BEO Extrapolation for Income Tax
[redacted]
C-1
What the BIR Is Alleging under the Relevant Schedule
[redacted]
C-2
Fatal Flaws: mixed computation base, unidentified invoice numbers, no third-party verification, lack of cost matching, and possible double counting
[redacted]
C-3
Documents from Printer/ATP Records and Company Records
[redacted]
D
Disallowed Expenses - BEO Percentage Rate
[redacted]
D-1
What the BIR Is Alleging
[redacted]
D-2
Issues: rate not prescribed, partial-year coverage, traceable cost of sales, and substantiation standard under Section 34(A)
[redacted]
D-3
Expense Category Documents and Substantiation Tracker
[redacted]
E
Disallowed Expenses Due to Alleged Non-Withholding of EWT
[redacted]
E-1
What the BIR Is Alleging
[redacted]
E-2
Issues: TWA status, scope of EWT, ITR/AFS vs. 1601-EQ gap, and subsequent withholding
[redacted]
E-3
Supplier Analysis and EWT Working Schedule
[redacted]
F
Disallowed Creditable Withholding Tax - Unsigned Forms 2307
[redacted]
F-1
What the BIR Is Alleging
[redacted]
F-2
Curable formal defect, double-taxation concern, and BIR system verification
[redacted]
F-3
Form 2307 Tracker and Supporting Documents
[redacted]
G
Disallowed Zero-Rated Sales
[redacted]
G-1
What the BIR Is Alleging
[redacted]
G-2
Zero-rating basis by transaction and customer classification review
[redacted]
G-3
Zero-Rated Sales Tracker
[redacted]
H
Disallowed Exempt Sales
[redacted]
H-1
What the BIR Is Alleging
[redacted]
H-2
Analysis, caution, and documents to gather
[redacted]
I
Alleged Missing Invoices - BEO Extrapolation for VAT
[redacted]
I-1
What the BIR Is Alleging under the VAT Schedule
[redacted]
I-2
Internal inconsistency between income-tax and VAT schedules
[redacted]
I-3
Arguments to Make
[redacted]
J
Disallowed Input Taxes
[redacted]
J-1
What the BIR Is Alleging
[redacted]
J-2
Unsupported expenses component and invoicing-defect component
[redacted]
J-3
Priority input-tax items and legal arguments
[redacted]
K
EWT Basic Tax Due
[redacted]
K-1
What the BIR Is Alleging
[redacted]
K-2
Computation Analysis
[redacted]
K-1A
Annex F - Detailed Analysis of Disallowed Input Taxes by Category
[redacted]
Categories reviewed: missing VAT labels, billing statements, no VAT amount, statements of account, wrong taxpayer name, delivery receipts, no name/TIN, exempt and non-VAT documents
[redacted]
K-2A
Date Anomalies Across BIR Annexes
[redacted]
Out-of-period invoices, duplicate invoice numbers, impossible dates, missing dates, and cascading effect on computations
[redacted]
L
Formal Reply Arguments, Jurisprudence, and EOPT Act Issues
[redacted]
L-0
Preliminary Reservation - Reply Is Not a Formal Protest
[redacted]
L-1
Governing Jurisprudence on BIR Assessments and Due Process
[redacted]
L-2
Effect of RA No. 11976 / Ease of Paying Taxes Act on Section 34(K)-based disallowance
[redacted]
L-3
TWA Status as Threshold Issue under RR No. 31-2020
[redacted]
L-4
Arithmetical Inconsistency in EWT Computation
[redacted]
L-5
Zero-Rated Sales - Wrong Legal Standard
[redacted]
L-6
Exempt Sales - Failure to Identify Transactions
[redacted]
L-7
Input VAT - General Labels Are Not Sufficient
[redacted]
L-8
Consolidated Request for Information from the BIR
[redacted]
L-9
Closing Argument: No PAN Should Be Issued Until Discrepancies Are Fully Itemized
[redacted]
Master
Master Table of Documents to Be Submitted by Taxpayer
[redacted]
Documents grouped by NOD annex, procedural issue, tax type, necessity, and financial impact
[redacted]
Phases
Suggested Submission Timeline and Binder Arrangement
[redacted]
Immediate NOD response, discussion of discrepancy, PAN stage, FLD/FAN stage, and binder arrangement
[redacted]
Page references are intentionally redacted because the full client report is confidential.
This article is a sample of work format only. It should not be treated as advice for any specific taxpayer, NOD, PAN, FAN, FLD, FDDA, or tax case. Each BIR audit must be evaluated using the actual Letter of Authority, Notice of Discrepancies, annexes, accounting records, tax returns, and supporting documents.