0000950170-24-127057 | 10-Q | XBRL Viewer

Commitments and Contingencies

9 Months Ended

Sep. 30, 2024

Commitments and Contingencies Disclosure [Abstract]

5. Commitments and Contingencies

Leases

The Company leases its offices and laboratory in Brisbane, California, or the Brisbane Lease, under a ten-year noncancelable lease agreement that ends in October 2031 with a ten-year renewable option. In November 2021, the Company subleased unoccupied space from December 2021 through November 2023, for aggregate sublease payments of $3.4 million. The sublease income, while it reduces the rent expense, is not considered in the value of the right-of-use assets or lease liabilities. The Company’s sublease income was zero and $0.6 million for the three months ended September 30, 2024 and 2023, respectively, and zero and $1.7 million for the nine months ended September 30, 2024 and 2023, respectively.

As of September 30, 2024, the operating lease right-of-use assets were $17.1 million and lease liabilities were $29.6 million on the unaudited condensed consolidated balance sheet. The weighted-average remaining lease term is 7.1 years.

The weighted-average incremental borrowing rate used to measure the operating lease liability is 8.4%.

Operating lease costs were $1.0 million and $0.5 million for the three months ended September 30, 2024 and 2023, respectively, and $2.9 million and $1.6 million for the nine months ended September 30, 2024 and 2023, respectively. Variable lease payments were $0.5 million and $0.4 million for the three months ended September 30, 2024 and 2023, respectively, and $1.7 million and $1.1 million for the nine months ended September 30, 2024 and 2023, respectively.

Future minimum lease payments and related lease liabilities as of September 30, 2024, were as follows:


	(in thousands)
2024 (remaining three months)	$	1,244
2025		5,065
2026		5,242
2027		5,425
2028 and thereafter		22,600
Total undiscounted lease payments		39,576
Less: Imputed interest		(9,969	)
Total	$	29,607

Guarantees and Indemnifications

In the normal course of business, the Company enters into agreements that contain a variety of representations and provide for general indemnification. The Company’s exposure under these agreements is unknown because it involves claims that may be made against the Company in the future. To date, the Company has not paid any claims or been required to defend any action related to its indemnification obligations. As of September 30, 2024, the Company did not have any material indemnification claims that were probable or reasonably possible and consequently has not recorded related liabilities.

Equity Incentive Plans (Tables)

9 Months Ended

Sep. 30, 2024

Share-Based Payment Arrangement [Abstract]

Summary of Stock Option Activity

The following table presents stock option activity under the Plans for the period:


	Number of Shares			Weighted- Average Exercise Price Per Share		Weighted- Average Remaining Contractual Term (in years)		Aggregate Intrinsic Value (in thousands)
Balances as of December 31, 2023		9,208,970		$	10.31		7.53	$	2,930
Stock options granted		4,710,324		$	5.70
Stock options exercised		(248,907	)	$	3.69
Stock options forfeited		(912,703	)	$	10.96
Balances as of September 30, 2024		12,757,684		$	8.69		7.79	$	8,435
Exercisable as of September 30, 2024		6,429,000		$	11.22		6.55	$	4,278

Summary of RSU Activity under 2020 Plan

A summary of RSU activity under the Company’s equity incentive plan and related information is as follows:


	Number of Shares			Weighted-Average Grant Date Fair Value Per Share
Unvested as of December 31, 2023		495,579		$	5.69
Granted		602,600			5.13
Vested		(187,835	)		5.59
Cancelled		(127,635	)		5.29
Unvested as of September 30, 2024		782,709		$	5.35

Summary of Stock-Based Compensation Expense

The total stock-based compensation expense recognized was as follows (in thousands):


	Three Months Ended September 30,				Nine Months Ended September 30,
	2024		2023		2024		2023
Research and development	$	2,325	$	2,243	$	6,918	$	6,801
General and administrative		2,284		2,306		7,293		7,015
Total stock-based compensation expense	$	4,609	$	4,549	$	14,211	$	13,816

Summary of Fair Value of Each Award Issued Estimated on the Date of Grant Using the Black-Scholes Option Pricing Model

The fair value of each stock option issued was estimated on the date of grant using the Black-Scholes option pricing model with the following assumptions:


	Three Months Ended September 30,		Nine Months Ended September 30,
	2024	2023	2024	2023
Expected term (in years)	6.02 - 6.08	6.08	6.02 - 6.08	5.50 - 6.08
Expected volatility	96.80% - 97.60%	81.80% - 81.90%	95.90% - 97.80%	81.20% - 82.40%
Risk-free interest rate	3.48% - 4.15%	4.20% - 4.42%	3.48% - 4.65%	3.47% - 4.42%
Dividend yield	—	—	—	—

Condensed Consolidated Statements of Stockholders' Equity (Parenthetical) - USD ($) $ in Thousands	3 Months Ended
	Jun. 30, 2024	Mar. 31, 2024	Mar. 31, 2023
Stock issuance costs	$ 480	$ 933
Common Stock and Prefunded Warrants [Member]
Stock issuance costs	$ 8,183
Related Party [Member]
Stock issuance costs			$ 525

Balance Sheet Components (Tables)

9 Months Ended

Sep. 30, 2024

Disclosure Of Balance Sheet Components [Abstract]

Schedule of Reconciliation of Cash, Cash Equivalents and Restricted Cash

The following table provides a reconciliation of cash, cash equivalents and restricted cash reported within the unaudited condensed consolidated balance sheets that sum to the total of the same amounts shown in the unaudited condensed consolidated statements of cash flows (in thousands):


	September 30, 2024		December 31, 2023
Cash	$	9,955	$	8,488
Cash equivalents		69,585		216,622
Cash and cash equivalents		79,540		225,110
Restricted cash		1,032		1,032
Cash, cash equivalents and restricted cash	$	80,572	$	226,142

Summary of Prepaid Expenses and Other Current Assets

Prepaid expenses and other current assets consisted of the following (in thousands):


	September 30, 2024		December 31, 2023
Prepaid research and development costs	$	2,300	$	2,617
Prepaid insurance		1,013		704
Prepaid and other current assets		863		823
Total prepaid expenses and other current assets	$	4,176	$	4,144

Summary of Property and Equipment, Net

Property and equipment, net, consisted of the following (in thousands):


	September 30, 2024			December 31, 2023
Leasehold improvements	$	17,254		$	17,245
Laboratory equipment		1,832			1,832
Furniture and fixtures		692			692
Computer equipment and software		33			33
Total property and equipment, gross		19,811			19,802
Less: accumulated depreciation		(6,642	)		(5,029	)
Total property and equipment, net	$	13,169		$	14,773

Summary of Accrued and Other Current Liabilities

Accrued and other current liabilities consisted of the following (in thousands):


	September 30, 2024		December 31, 2023
Accrued research and development expenses	$	4,704	$	4,027
Accrued compensation		4,389		5,607
Accrued professional services		1,562		501
Other accrued and current liabilities		206		141
Total accrued and other current liabilities	$	10,861	$	10,276

Commitments and Contingencies - Additional Information (Detail)	1 Months Ended	3 Months Ended		9 Months Ended		24 Months Ended
	Nov. 30, 2021	Sep. 30, 2024 USD ($) Claim	Sep. 30, 2023 USD ($)	Sep. 30, 2024 USD ($) Claim	Sep. 30, 2023 USD ($)	Nov. 30, 2023 USD ($)	Dec. 31, 2023 USD ($)
Gain Contingencies [Line Items]
Aggregate sublease payment receivable						$ 3,400,000
Sublease income		$ 0	$ 600,000	$ 0	$ 1,700,000
Operating lease right-of-use asset		17,050,000		17,050,000			$ 18,009,000
Lease liabilities		$ 29,607,000		$ 29,607,000
Weighted average incremental borrowing rate		8.40%		8.40%
Operating lease costs		$ 1,000,000	500,000	$ 2,900,000	1,600,000
Variable lease payments		500,000	$ 400,000	1,700,000	$ 1,100,000
Loss contingency accrual		$ 0		$ 0
Indemnification Agreement [Member]
Gain Contingencies [Line Items]
Loss contingency pending claims \| Claim		0		0
Brisbane, California [Member]
Gain Contingencies [Line Items]
Operating lease, term of contract		10 years		10 years
Operating lease, expiration month and year				2031-10
Operating lease, renewal term		10 years		10 years
Lessee, Operating Sublease Commencement Year and Month	2021-12
Lessee operating sublease expiration year and month	2023-11
Operating lease right-of-use asset		$ 17,100,000		$ 17,100,000
Lease liabilities		$ 29,600,000		$ 29,600,000
Weighted average remaining lease term		7 years 1 month 6 days		7 years 1 month 6 days

Net Loss Per Share

9 Months Ended

Sep. 30, 2024

Earnings Per Share [Abstract]

Net Loss Per Share

8. Net Loss Per Share

The Company calculates basic net loss per share by dividing net loss by the weighted-average number of shares of common stock outstanding, excluding restricted common stock. The weighted-average number of shares of common stock used in the basic and diluted net loss per share calculation include pre-funded warrants to purchase up to 41,283,052 shares of common stock, as the pre-funded warrants are exercisable at any time for nominal cash consideration. The Company has generated a net loss in all periods presented, so the basic and diluted net loss per share are the same, as the inclusion of the potentially dilutive securities would be anti-dilutive.

The following outstanding potentially dilutive shares have been excluded from the calculation of diluted net loss per share due to their anti-dilutive effect:


	Three Months Ended September 30,				Nine Months Ended September 30,
	2024		2023		2024		2023
Stock options to purchase common stock		12,757,684		9,335,202		12,757,684		9,335,202
Shares subject to Employee Stock Purchase Plan		36,364		97,880		36,364		97,880
Unvested restricted stock units		782,709		533,917		782,709		533,917
Common warrants		8,104,615		8,427,508		8,104,615		8,427,508
Total		21,681,372		18,394,507		21,681,372		18,394,507

Equity Incentive Plans - Summary of RSU Activity under 2020 Plan (Detail)	9 Months Ended
	Sep. 30, 2024 $ / shares shares
Share-Based Payment Arrangement [Abstract]
Number of Shares, Unvested as of December 31, 2023 \| shares	495,579
Number of Shares, Granted \| shares	602,600
Number of Shares, Vested \| shares	(187,835)
Number of Shares, Cancelled \| shares	(127,635)
Number of Shares, Unvested as of March 31, 2024 \| shares	782,709
Weighted-Average Grant Date Fair Value Per Share, Granted Unvested as of December 31, 2023 \| $ / shares	$ 5.69
Weighted-Average Grant Date Fair Value Per Share, Granted \| $ / shares	5.13
Weighted-Average Grant Date Fair Value Per Share, Vested \| $ / shares	5.59
Weighted-Average Grant Date Fair Value Per Share, Cancelled \| $ / shares	5.29
Weighted-Average Grant Date Fair Value Per Share, Granted Unvested as of March 31, 2024 \| $ / shares	$ 5.35

Balance Sheet Components

9 Months Ended

Sep. 30, 2024

Disclosure Of Balance Sheet Components [Abstract]

Balance Sheet Components

4. Balance Sheet Components

Cash, Cash Equivalents and Restricted Cash

The Company considers all highly liquid instruments with an original maturity of three months or less at time of purchase to be cash equivalents. Cash equivalents, which include amounts invested in money market funds, are stated at fair value.

Restricted cash as of September 30, 2024 relates to the letters of credit established for the Company’s office leases.


	September 30, 2024		December 31, 2023
Cash	$	9,955	$	8,488
Cash equivalents		69,585		216,622
Cash and cash equivalents		79,540		225,110
Restricted cash		1,032		1,032
Cash, cash equivalents and restricted cash	$	80,572	$	226,142

Prepaid Expenses and Other Current Assets

Prepaid expenses and other current assets consisted of the following (in thousands):


	September 30, 2024		December 31, 2023
Prepaid research and development costs	$	2,300	$	2,617
Prepaid insurance		1,013		704
Prepaid and other current assets		863		823
Total prepaid expenses and other current assets	$	4,176	$	4,144

Property and Equipment, Net

Property and equipment, net, consisted of the following (in thousands):


	September 30, 2024			December 31, 2023
Leasehold improvements	$	17,254		$	17,245
Laboratory equipment		1,832			1,832
Furniture and fixtures		692			692
Computer equipment and software		33			33
Total property and equipment, gross		19,811			19,802
Less: accumulated depreciation		(6,642	)		(5,029	)
Total property and equipment, net	$	13,169		$	14,773

The Company recognized depreciation for property and equipment of $0.5 million for each of the three months ended September 30, 2024 and 2023, and $1.6 million for each of the nine months ended September 30, 2024 and 2023.

Accrued and Other Current Liabilities

Accrued and other current liabilities consisted of the following (in thousands):


	September 30, 2024		December 31, 2023
Accrued research and development expenses	$	4,704	$	4,027
Accrued compensation		4,389		5,607
Accrued professional services		1,562		501
Other accrued and current liabilities		206		141
Total accrued and other current liabilities	$	10,861	$	10,276

Balance Sheet Components - Summary of Prepaid Expenses and Other Current Assets (Detail) - USD ($) $ in Thousands	Sep. 30, 2024	Dec. 31, 2023
Prepaid Expense and Other Assets, Current [Abstract]
Prepaid research and development costs	$ 2,300	$ 2,617
Prepaid insurance	1,013	704
Prepaid and other current assets	863	823
Total prepaid expenses and other current assets	$ 4,176	$ 4,144

Fair Value Measurements - Summary of Financial Assets Measured at Fair Value on a Recurring Basis (Detail) - USD ($) $ in Thousands	Sep. 30, 2024	Dec. 31, 2023
Fair Value Assets And Liabilities Measured On Recurring And Nonrecurring Basis [Line Items]
Amortized Cost	$ 330,006	$ 251,218
Gross Unrealized Holding Gains	158	10
Gross Unrealized Holding Losses	(3)
Aggregate Fair Value	330,161	251,228
Level 1 [Member] \| Cash and Cash Equivalents [Member] \| Money Market Funds [Member]
Fair Value Assets And Liabilities Measured On Recurring And Nonrecurring Basis [Line Items]
Amortized Cost	40,679	143,933
Aggregate Fair Value	40,679	143,933
Level 2 [Member] \| Cash and Cash Equivalents [Member]
Fair Value Assets And Liabilities Measured On Recurring And Nonrecurring Basis [Line Items]
Amortized Cost	69,585	216,622
Aggregate Fair Value	69,585	216,622
Level 2 [Member] \| Cash and Cash Equivalents [Member] \| Government Bonds [Member]
Fair Value Assets And Liabilities Measured On Recurring And Nonrecurring Basis [Line Items]
Amortized Cost	28,906	72,689
Aggregate Fair Value	28,906	72,689
Level 2 [Member] \| Short-Term Investments [Member]
Fair Value Assets And Liabilities Measured On Recurring And Nonrecurring Basis [Line Items]
Amortized Cost	260,421	34,596
Gross Unrealized Holding Gains	158	10
Gross Unrealized Holding Losses	(3)
Aggregate Fair Value	260,576	34,606
Level 2 [Member] \| Short-Term Investments [Member] \| Government Bonds [Member]
Fair Value Assets And Liabilities Measured On Recurring And Nonrecurring Basis [Line Items]
Amortized Cost	260,421	34,596
Gross Unrealized Holding Gains	158	10
Gross Unrealized Holding Losses	(3)
Aggregate Fair Value	$ 260,576	$ 34,606

Pay vs Performance Disclosure - USD ($) $ in Thousands	3 Months Ended						9 Months Ended
Pay vs Performance Disclosure - USD ($) $ in Thousands	Sep. 30, 2024	Jun. 30, 2024	Mar. 31, 2024	Sep. 30, 2023	Jun. 30, 2023	Mar. 31, 2023	Sep. 30, 2024	Sep. 30, 2023
Pay vs Performance Disclosure
Net Income (Loss)	$ (34,824)	$ (29,610)	$ (25,176)	$ (32,482)	$ (35,188)	$ (38,676)	$ (89,610)	$ (106,346)

- Definition

The portion of profit or loss for the period, net of income taxes, which is attributable to the parent.

+ References

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-Subparagraph (SX 210.13-02(a)(5))
-Publisher FASB
-URI https://asc.fasb.org/1943274/2147480097/470-10-S99-1B

Reference 32: http://www.xbrl.org/2003/role/disclosureRef
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-Paragraph 60B
-Subparagraph (a)
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Reference 33: http://www.xbrl.org/2003/role/disclosureRef
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-Subparagraph (SX 210.9-04(22))
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-URI https://asc.fasb.org/1943274/2147478524/942-220-S99-1

+ Details

Net Loss Per Share - Additional Information (Detail)	Sep. 30, 2024 shares
Maximum [Member] \| Common Stock [Member]
Class of Warrant or Right [Line Items]
Warrants exercised	41,283,052

Commitments and Contingencies - Future Minimum Lease Payments and Related Lease Liabilities (Detail) $ in Thousands	Sep. 30, 2024 USD ($)
Commitments and Contingencies Disclosure [Abstract]
2024 (remaining three months)	$ 1,244
2025	5,065
2026	5,242
2027	5,425
2028 and thereafter	22,600
Total undiscounted lease payments	39,576
Less: Imputed interest	(9,969)
Lease liabilities	$ 29,607

Equity Incentive Plans - Summary of Stock-Based Compensation Expense (Detail) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2024	Sep. 30, 2023	Sep. 30, 2024	Sep. 30, 2023
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Total stock-based compensation expense	$ 4,609	$ 4,549	$ 14,211	$ 13,816
Research and Development [Member]
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Total stock-based compensation expense	2,325	2,243	6,918	6,801
General and Administrative [Member]
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Total stock-based compensation expense	$ 2,284	$ 2,306	$ 7,293	$ 7,015

- Definition

Line items represent financial concepts included in a table. These concepts are used to disclose reportable information associated with domain members defined in one or many axes to the table.

+ References

Reference 1: http://www.xbrl.org/2003/role/disclosureRef
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Reference 3: http://www.xbrl.org/2003/role/disclosureRef
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Reference 4: http://www.xbrl.org/2003/role/disclosureRef
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Reference 8: http://www.xbrl.org/2003/role/disclosureRef
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Reference 9: http://www.xbrl.org/2003/role/disclosureRef
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Reference 19: http://www.xbrl.org/2003/role/disclosureRef
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+ Details

Fair Value Measurements - Additional Information (Details)	Sep. 30, 2024 USD ($)
Fair Value Disclosures [Abstract]
Credit losses	$ 0
Allowance for doubtful accounts	0
Unrealized loss position for more than 12 months	$ 0

Basis of Presentation and Significant Accounting Policies

9 Months Ended

Sep. 30, 2024

Accounting Policies [Abstract]

Basis of Presentation and Significant Accounting Policies

2. Basis of Presentation and Significant Accounting Policies

Basis of Presentation

The accompanying unaudited condensed consolidated financial statements have been prepared in accordance with generally accepted accounting principles in the United States, or GAAP, and applicable rules and regulations of the SEC regarding interim financial reporting.

The condensed consolidated balance sheet as of September 30, 2024, the condensed consolidated statements of operations, comprehensive loss, stockholders’ equity for the three and nine months ended September 30, 2024 and 2023 and the condensed consolidated statements of cash flows for the nine months ended September 30, 2024 and 2023 are unaudited. These unaudited condensed consolidated financial statements have been prepared on the same basis as the annual consolidated financial statements and, in the opinion of management, reflect all adjustments, which include only normal recurring adjustments, necessary to present fairly the Company’s consolidated financial position, results of operations and cash flows for the interim period presented. The financial data and the other financial information contained in these notes to the condensed consolidated financial statements related to the three-month periods are also unaudited. The results of operations for the three and nine months ended September 30, 2024 are not necessarily indicative of the results to be expected for the year ending December 31, 2024 or for any other future annual or interim period. The condensed consolidated balance sheet as of December 31, 2023 included herein was derived from the audited financial statements as of that date. These unaudited condensed consolidated financial statements should be read in conjunction with the Company's audited consolidated financial statements included in the Company’s Annual Report on Form 10-K for the year ended December 31, 2023, filed with the SEC on March 26, 2024.

Use of Estimates

The preparation of financial statements in conformity with accounting principles generally accepted in the United States of America, or GAAP, requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities and disclosure of contingent assets and liabilities at the date of the financial statements and the reported expenses during the reporting period. Management evaluates its estimates, including but not limited to the fair value of investments, operating lease right-of-use assets and liabilities, valuation of deferred tax assets and uncertain tax positions (including valuation allowance), clinical trial accruals and

stock-based compensation. The Company evaluates its estimates and assumptions on an ongoing basis using historical experience and other factors and adjusts those estimates and assumptions when facts and circumstances dictate. Actual results could differ from those estimates.

Principles of Consolidation

The condensed consolidated financial statements include the operations of Annexon, Inc. and its wholly-owned subsidiary and include the results of operations and cash flows of these entities. All intercompany balances and transactions have been eliminated in consolidation.

Summary of Significant Accounting Policies

Reference is made to Note 2, Summary of Significant Accounting Policies, in the Company’s 2023 Form 10-K filed on March 26, 2024 for a detailed description of significant accounting policies. There have been no significant changes to the Company’s accounting policies as disclosed in its 2023 Form 10-K.

Recently Issued Accounting Pronouncements

In November 2023, the Financial Accounting Standards Board (FASB) issued Accounting Standards Update (ASU) 2023-07, Segment Reporting: Improvements to Reportable Segment Disclosures, which requires disclosure of incremental segment information on an interim and annual basis. This ASU is effective for fiscal years beginning after December 15, 2023, and interim periods within fiscal periods beginning after December 15, 2024, and requires retrospective application to all prior periods presented in the financial statements. The Company adopted annual requirements under ASU 2023-07 on January 1, 2024 and plans to adopt interim requirements under ASU 2023-07 on January 1, 2025. The Company will begin including financial statement disclosures in accordance with ASU 2023-07 in its Annual Report on Form 10-K for the year ended December 31, 2024. The Company is evaluating the impact of this guidance on its financial statements and related disclosures.

In December 2023, the FASB issued ASU 2023-09, Income Taxes: Improvements to Income Tax Disclosures, which requires enhanced annual disclosures regarding the rate reconciliation and income taxes paid information. ASU 2023-09 is effective for fiscal years beginning after December 15, 2024 and may be adopted on a prospective or retrospective basis. Early adoption is permitted. The Company is evaluating the impact of this guidance on its financial statements and related disclosures.

Balance Sheet Components - Summary of Property and Equipment, Net (Detail) - USD ($) $ in Thousands	Sep. 30, 2024	Dec. 31, 2023
Property Plant And Equipment [Line Items]
Total property and equipment, gross	$ 19,811	$ 19,802
Less: accumulated depreciation	(6,642)	(5,029)
Total property and equipment, net	13,169	14,773
Leasehold Improvements [Member]
Property Plant And Equipment [Line Items]
Total property and equipment, gross	17,254	17,245
Laboratory Equipment [Member]
Property Plant And Equipment [Line Items]
Total property and equipment, gross	1,832	1,832
Furniture and Fixtures [Member]
Property Plant And Equipment [Line Items]
Total property and equipment, gross	692	692
Computer Equipment and Software [Member]
Property Plant And Equipment [Line Items]
Total property and equipment, gross	$ 33	$ 33

Commitments and Contingencies (Tables)

9 Months Ended

Sep. 30, 2024

Commitments and Contingencies Disclosure [Abstract]

Future Minimum Lease Payments and Related Lease Liabilities

Future minimum lease payments and related lease liabilities as of September 30, 2024, were as follows:


	(in thousands)
2024 (remaining three months)	$	1,244
2025		5,065
2026		5,242
2027		5,425
2028 and thereafter		22,600
Total undiscounted lease payments		39,576
Less: Imputed interest		(9,969	)
Total	$	29,607

Condensed Consolidated Statements of Operations - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2024	Sep. 30, 2023	Sep. 30, 2024	Sep. 30, 2023
Operating expenses:
Research and development	$ 30,105	$ 27,893	$ 76,094	$ 90,489
General and administrative	9,337	6,888	25,500	23,225
Total operating expenses	39,442	34,781	101,594	113,714
Loss from operations	(39,442)	(34,781)	(101,594)	(113,714)
Interest and other income, net	4,618	2,299	11,984	7,368
Net loss	$ (34,824)	$ (32,482)	$ (89,610)	$ (106,346)
Net loss per share, basic	$ (0.25)	$ (0.43)	$ (0.68)	$ (1.42)
Net loss per share, diluted	$ (0.25)	$ (0.43)	$ (0.68)	$ (1.42)
Weighted-average shares used in computing net loss per share, basic	139,933,019	75,342,495	130,945,980	74,815,274
Weighted-average shares used in computing net loss per share, diluted	139,933,019	75,342,495	130,945,980	74,815,274

Condensed Consolidated Statements of Comprehensive Loss - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2024	Sep. 30, 2023	Sep. 30, 2024	Sep. 30, 2023
Statement of Comprehensive Income [Abstract]
Net loss	$ (34,824)	$ (32,482)	$ (89,610)	$ (106,346)
Other comprehensive income (loss):
Foreign currency translation adjustment	2	(2)	(9)	(8)
Unrealized gain on available-for-sale securities	164	50	138	257
Comprehensive loss	$ (34,658)	$ (32,434)	$ (89,481)	$ (106,097)

- Definition

Amount after tax of increase (decrease) in equity from transactions and other events and circumstances from net income and other comprehensive income, attributable to parent entity. Excludes changes in equity resulting from investments by owners and distributions to owners.

+ References + Details

- Definition

The portion of profit or loss for the period, net of income taxes, which is attributable to the parent.

+ References

+ Details

Balance Sheet Components - Additional Information (Detail) - USD ($) $ in Millions	3 Months Ended		9 Months Ended
	Sep. 30, 2024	Sep. 30, 2023	Sep. 30, 2024	Sep. 30, 2023
Prepaid Expense and Other Assets, Current [Abstract]
Depreciation expense	$ 0.5	$ 0.5	$ 1.6	$ 1.6

Stockholder's Equity - Summary of Warrants Activity (Detail) - $ / shares	9 Months Ended
	Sep. 30, 2024	Sep. 30, 2023
Number of Common Warrants [Member]
Class of Warrant or Right [Line Items]
Beginning Balance	8,427,508	8,427,508
Exercised	(322,893)
Ending Balance	8,104,615	8,427,508
Number of Pre-funded Warrants [Member]
Class of Warrant or Right [Line Items]
Beginning Balance	40,492,923	24,696,206
Issued	7,000,000
Exercised	(6,209,871)	(2,583,144)
Ending Balance	41,283,052	22,113,062
Common Warrant and Pre-funded Warrants [Member]
Class of Warrant or Right [Line Items]
Weighted-Average Exercise Price, Issued	$ 0.001
Weighted-Average Exercise Price, Exercised	$ 0.307	$ 0.001

Cover Page - shares	9 Months Ended
Cover Page - shares	Sep. 30, 2024	Nov. 11, 2024
Document Information [Line Items]
Document Type	10-Q
Document Quarterly Report	true
Document Transition Report	false
Amendment Flag	false
Document Period End Date	Sep. 30, 2024
Document Fiscal Year Focus	2024
Document Fiscal Period Focus	Q3
Trading Symbol	ANNX
Entity Registrant Name	ANNEXON, INC.
Entity Central Index Key	0001528115
Current Fiscal Year End Date	--12-31
Entity Current Reporting Status	Yes
Entity Interactive Data Current	Yes
Entity Filer Category	Non-accelerated Filer
Title of 12(b) Security	Common Stock, par value $0.001 per share
Security Exchange Name	NASDAQ
Entity File Number	001-39402
Entity Incorporation, State or Country Code	DE
Entity Tax Identification Number	27-5414423
Entity Address, Address Line One	1400 Sierra Point Parkway
Entity Address, Address Line Two	Bldg C
Entity Address, Address Line Three	Suite 200
Entity Address, City or Town	Brisbane
Entity Address, State or Province	CA
Entity Address, Postal Zip Code	94005
City Area Code	650
Local Phone Number	822-5500
Entity Small Business	true
Entity Emerging Growth Company	false
Entity Shell Company	false
Common Stock [Member]
Document Information [Line Items]
Entity Common Stock, Shares Outstanding		106,593,505
Prefunded Warrant [Member]
Document Information [Line Items]
Entity Common Stock, Shares Outstanding		41,283,052

Fair Value Measurements (Tables)

9 Months Ended

Sep. 30, 2024

Fair Value Disclosures [Abstract]

Summary of Financial Assets Measured at Fair Value on a Recurring Basis

The following tables summarize the fair value of the Company’s financial assets measured at fair value on a recurring basis by level within the fair value hierarchy (in thousands):


		September 30, 2024
	Valuation Hierarchy	Amortized Cost		Gross Unrealized Holding Gains		Gross Unrealized Holding Losses			Aggregate Fair Value
Assets:
Cash equivalents:
Money market funds	Level 1	$	40,679	$	—	$	—		$	40,679
Government bonds	Level 2		28,906		—		—			28,906
Total cash equivalents			69,585		—		—			69,585
Short-term investments:
Government bonds	Level 2		260,421		158		(3	)		260,576
Total short-term investments			260,421		158		(3	)		260,576
		$	330,006	$	158	$	(3	)	$	330,161


		December 31, 2023
	Valuation Hierarchy	Amortized Cost		Gross Unrealized Holding Gains		Gross Unrealized Holding Losses		Aggregate Fair Value
Assets:
Cash equivalents:
Money market funds	Level 1	$	143,933	$	—	$	—	$	143,933
Government bonds	Level 2		72,689		—		—		72,689
Total cash equivalents			216,622		—		—		216,622
Short-term investments:
Government bonds	Level 2		34,596		10		—		34,606
Total short-term investments			34,596		10		—		34,606
		$	251,218	$	10	$	—	$	251,228

Stockholder's Equity

9 Months Ended

Sep. 30, 2024

Stockholders' Equity Note [Abstract]

Stockholders' Equity

6. Stockholders’ Equity

2024 Financing

In June 2024, the Company raised net proceeds of approximately $116.8 million after deducting underwriting discounts and offering expenses through the sale of 13,001,120 shares of the Company’s common stock, par value $0.001 per share at a price of $6.25 per share and pre-funded warrants to purchase an aggregate of 7,000,000 shares of common stock at a price of $6.249 per share, which equals the per share offering price for the shares of common stock less the $0.001 exercise price for each pre-funded warrant. The pre-funded warrants are immediately exercisable, subject to certain beneficial ownership limitations. The warrants meet the criteria for equity classification and were therefore recorded at fair value as of the grant date as a component of stockholders’ equity within additional paid-in capital in the amount of $43.7 million.

2023 Financing

In December 2023, the Company raised net proceeds of approximately $117.0 million after deducting underwriting discounts and offering expenses through the sale of 25,035,000 shares of the Company’s common stock, par value $0.001 per share at a price of $2.880

per share and pre-funded warrants to purchase an aggregate of 18,379,861 shares of common stock at a price of $2.879 per share, which equals the per share offering price for the shares of common stock less the $0.001 exercise price for each pre-funded warrant. An entity related to one of the Company’s directors participated in the public offering and purchased 350,000 shares of common stock for an aggregate price of approximately $1.0 million. The pre-funded warrants are immediately exercisable, subject to certain beneficial ownership limitations. The warrants meet the criteria for equity classification and were therefore recorded at fair value as of the grant date as a component of stockholders’ equity within additional paid-in capital in the amount of $52.9 million. The Company issued an aggregate of 5,243,400 shares and 965,427 shares of common stock upon the cashless and cash exercise of these pre-funded warrants in February 2024 and April 2024, respectively.

2022 Financing

In July 2022, the Company raised net proceeds of approximately $122.5 million after deducting fees and expenses through the sale of an aggregate of 9,013,834 shares of common stock, pre-funded warrants to purchase up to 24,696,206 shares of its common stock and accompanying common warrants to purchase up to 8,427,508 shares of its common stock. The offering price per share and accompanying common warrant was $3.87125 per share and the offering price per pre-funded warrant and accompanying common warrant was $3.87025 per share, which equals the per share offering price for the shares of common stock less the $0.001 exercise price for each such pre-funded warrant. The pre-funded warrants remain exercisable until exercised in full. The common warrants have an exercise price of $5.806875 per share and expire on June 30, 2025. Both the pre-funded and common warrants are immediately exercisable, subject to beneficial ownership limitations. The warrants meet the criteria for equity classification and were therefore recorded at fair value as of the grant date as a component of stockholders’ equity within additional paid-in capital. The Company issued an aggregate of 2,582,557 shares of common stock upon the cashless exercise of the pre-funded warrants in March 2023. The Company issued an aggregate of 19,901 shares of common stock upon the cashless exercise of the common warrants in June 2024. Subsequent to September 30, 2024 and through the date of issuance of these interim unaudited condensed financial statements, the Company issued an aggregate of 2,739,096 shares of common stock upon the cashless exercise of the pre-funded warrants.

Pre-Funded and Common Warrants

The following summarizes warrant activity during the nine months ended September 30, 2024 and 2023:


	Number of Common Warrants			Number of Pre-funded Warrants			Weighted-Average Exercise Price
Balances as of December 31, 2023		8,427,508			40,492,923
Issued		—			7,000,000		$	0.001
Exercised		(322,893	)		(6,209,871	)	$	0.307
Balances as of September 30, 2024		8,104,615			41,283,052


	Number of Common Warrants		Number of Pre-funded Warrants			Weighted-Average Exercise Price
Balances as of December 31, 2022		8,427,508		24,696,206
Exercised		—		(2,583,144	)	$	0.001
Balances as of September 30, 2023		8,427,508		22,113,062

2024 At-the-Market (ATM) Program

In March 2024, the Company entered into a sales agreement with Cowen and Company LLC, or TD Cowen, as sales agent, or 2024 ATM program, pursuant to which the Company may issue and sell shares of its common stock for an aggregate maximum offering of $100.0 million. TD Cowen is entitled to compensation up to 3% of the aggregate gross proceeds for the common stock sold through the 2024 ATM program. As of September 30, 2024, the Company has not made any sales under the 2024 ATM program. Subsequent to September 30, 2024 and through the date of issuance of these interim unaudited condensed financial statements, the Company sold 750,000 shares of common stock under the 2024 ATM for net proceeds of approximately $4.5 million, after deducting commissions paid to TD Cowen.

2021 ATM Program

In August 2021, the Company entered into a sales agreement with TD Cowen, as sales agent, pursuant to which the Company may issue and sell shares of its common stock for an aggregate maximum offering of $100.0 million under an at-the-market offering

program, or 2021 ATM program. TD Cowen is entitled to compensation up to 3% of the aggregate gross proceeds for the common stock sold through the 2021 ATM program. During the nine months ended September 30, 2024 and 2023, the Company sold 7,576,067 shares and 2,646,458 shares of common stock, respectively, under the 2021 ATM program for net proceeds of approximately $38.4 million and $17.5 million, respectively, after deducting commissions paid to TD Cowen. The Form S-3 registration statement pursuant to which the 2021 ATM Program is registered expired on August 15, 2024, and no shares of common stock may be sold under the 2021 ATM Program after that date.

Common Stock

The Company reserved the following shares of common stock for issuance as follows:


	September 30, 2024		December 31, 2023
Stock options issued and outstanding		12,757,684		9,208,970
Stock options reserved for 2020 Incentive Award Plan		2,059,871		1,988,340
Unvested restricted stock units outstanding		782,709		495,579
Common stock reserved for 2021 ATM program		—		2,619,471
Common stock reserved for 2024 ATM program		25,000,000		—
Common stock reserved for Employee Stock Purchase Plan		2,023,537		1,338,381
Common stock reserved for 2022 Employment Inducement Award Plan		2,398,730		758,084
Common stock reserved for pre-funded warrants		41,283,052		40,493,510
Common stock reserved for common warrants		8,104,615		8,427,508
Total common stock reserved		94,410,198		65,329,843

- Definition

The entire disclosure for equity.

+ References

Reference 1: http://www.xbrl.org/2003/role/disclosureRef
-Topic 505
-SubTopic 10
-Name Accounting Standards Codification
-Section 50
-Paragraph 13
-Subparagraph (b)
-Publisher FASB
-URI https://asc.fasb.org/1943274/2147481112/505-10-50-13

Reference 2: http://www.xbrl.org/2003/role/disclosureRef
-Topic 505
-SubTopic 10
-Name Accounting Standards Codification
-Section 50
-Paragraph 13
-Subparagraph (h)
-Publisher FASB
-URI https://asc.fasb.org/1943274/2147481112/505-10-50-13

Reference 3: http://www.xbrl.org/2003/role/disclosureRef
-Topic 505
-SubTopic 10
-Name Accounting Standards Codification
-Section 50
-Paragraph 14
-Subparagraph (b)
-Publisher FASB
-URI https://asc.fasb.org/1943274/2147481112/505-10-50-14

Reference 4: http://www.xbrl.org/2003/role/disclosureRef
-Topic 946
-SubTopic 235
-Name Accounting Standards Codification
-Section 50
-Paragraph 2
-Subparagraph (a)
-Publisher FASB
-URI https://asc.fasb.org/1943274/2147477968/946-235-50-2

Reference 5: http://www.xbrl.org/2003/role/disclosureRef
-Topic 946
-SubTopic 235
-Name Accounting Standards Codification
-Section 50
-Paragraph 2
-Subparagraph (d)
-Publisher FASB
-URI https://asc.fasb.org/1943274/2147477968/946-235-50-2

Reference 6: http://www.xbrl.org/2003/role/disclosureRef
-Topic 946
-SubTopic 505
-Name Accounting Standards Codification
-Section 50
-Paragraph 6
-Publisher FASB
-URI https://asc.fasb.org/1943274/2147478448/946-505-50-6

Reference 7: http://www.xbrl.org/2003/role/disclosureRef
-Topic 815
-SubTopic 40
-Name Accounting Standards Codification
-Section 50
-Paragraph 6
-Subparagraph (a)
-Publisher FASB
-URI https://asc.fasb.org/1943274/2147480237/815-40-50-6

Reference 8: http://www.xbrl.org/2003/role/disclosureRef
-Topic 505
-SubTopic 10
-Name Accounting Standards Codification
-Section S99
-Paragraph 1
-Subparagraph (SX 210.3-04)
-Publisher FASB
-URI https://asc.fasb.org/1943274/2147480008/505-10-S99-1

Reference 9: http://www.xbrl.org/2003/role/disclosureRef
-Topic 235
-SubTopic 10
-Name Accounting Standards Codification
-Section S99
-Paragraph 1
-Subparagraph (SX 210.4-08(e)(1))
-Publisher FASB
-URI https://asc.fasb.org/1943274/2147480678/235-10-S99-1

Reference 10: http://fasb.org/us-gaap/role/ref/legacyRef
-Topic 505
-Name Accounting Standards Codification
-Publisher FASB
-URI https://asc.fasb.org/505/tableOfContent

Reference 11: http://www.xbrl.org/2003/role/disclosureRef
-Topic 505
-SubTopic 10
-Name Accounting Standards Codification
-Section 50
-Paragraph 13
-Publisher FASB
-URI https://asc.fasb.org/1943274/2147481112/505-10-50-13

Reference 12: http://www.xbrl.org/2003/role/disclosureRef
-Topic 505
-SubTopic 10
-Name Accounting Standards Codification
-Section 50
-Paragraph 13
-Subparagraph (g)
-Publisher FASB
-URI https://asc.fasb.org/1943274/2147481112/505-10-50-13

Reference 13: http://www.xbrl.org/2003/role/disclosureRef
-Topic 505
-SubTopic 10
-Name Accounting Standards Codification
-Section 50
-Paragraph 13
-Subparagraph (i)
-Publisher FASB
-URI https://asc.fasb.org/1943274/2147481112/505-10-50-13

Reference 14: http://www.xbrl.org/2003/role/disclosureRef
-Topic 505
-SubTopic 10
-Name Accounting Standards Codification
-Section 50
-Paragraph 14
-Subparagraph (a)
-Publisher FASB
-URI https://asc.fasb.org/1943274/2147481112/505-10-50-14

Reference 15: http://www.xbrl.org/2003/role/disclosureRef
-Topic 505
-SubTopic 10
-Name Accounting Standards Codification
-Section 50
-Paragraph 14
-Subparagraph (c)
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-URI https://asc.fasb.org/1943274/2147481112/505-10-50-14

Reference 16: http://www.xbrl.org/2003/role/disclosureRef
-Topic 505
-SubTopic 10
-Name Accounting Standards Codification
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-Publisher FASB
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Reference 17: http://www.xbrl.org/2003/role/disclosureRef
-Topic 505
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-Name Accounting Standards Codification
-Section 50
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-Subparagraph (a)
-Publisher FASB
-URI https://asc.fasb.org/1943274/2147481112/505-10-50-18

Reference 18: http://www.xbrl.org/2003/role/disclosureRef
-Topic 505
-SubTopic 10
-Name Accounting Standards Codification
-Section 50
-Paragraph 18
-Subparagraph (b)
-Publisher FASB
-URI https://asc.fasb.org/1943274/2147481112/505-10-50-18

Reference 19: http://www.xbrl.org/2003/role/disclosureRef
-Topic 505
-SubTopic 10
-Name Accounting Standards Codification
-Section 50
-Paragraph 18
-Subparagraph (d)
-Publisher FASB
-URI https://asc.fasb.org/1943274/2147481112/505-10-50-18

+ Details

Stockholder's Equity (Tables)

9 Months Ended

Sep. 30, 2024

Stockholders' Equity Note [Abstract]

Summary of Warrants Activity

The following summarizes warrant activity during the nine months ended September 30, 2024 and 2023:


	Number of Common Warrants			Number of Pre-funded Warrants			Weighted-Average Exercise Price
Balances as of December 31, 2023		8,427,508			40,492,923
Issued		—			7,000,000		$	0.001
Exercised		(322,893	)		(6,209,871	)	$	0.307
Balances as of September 30, 2024		8,104,615			41,283,052


	Number of Common Warrants		Number of Pre-funded Warrants			Weighted-Average Exercise Price
Balances as of December 31, 2022		8,427,508		24,696,206
Exercised		—		(2,583,144	)	$	0.001
Balances as of September 30, 2023		8,427,508		22,113,062

Schedule of Common Stock Reserved for Future Issuance

The Company reserved the following shares of common stock for issuance as follows:


	September 30, 2024		December 31, 2023
Stock options issued and outstanding		12,757,684		9,208,970
Stock options reserved for 2020 Incentive Award Plan		2,059,871		1,988,340
Unvested restricted stock units outstanding		782,709		495,579
Common stock reserved for 2021 ATM program		—		2,619,471
Common stock reserved for 2024 ATM program		25,000,000		—
Common stock reserved for Employee Stock Purchase Plan		2,023,537		1,338,381
Common stock reserved for 2022 Employment Inducement Award Plan		2,398,730		758,084
Common stock reserved for pre-funded warrants		41,283,052		40,493,510
Common stock reserved for common warrants		8,104,615		8,427,508
Total common stock reserved		94,410,198		65,329,843

Condensed Consolidated Statements of Cash Flows - USD ($) $ in Thousands	9 Months Ended
	Sep. 30, 2024	Sep. 30, 2023
Operating activities:
Net loss	$ (89,610)	$ (106,346)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization	1,613	1,610
Accretion of discount on available-for-sale securities	(6,032)	(2,290)
Stock-based compensation	14,211	13,816
Reduction in the carrying amount of right-of-use assets	959	823
Changes in operating assets and liabilities:
Prepaid expenses and other current assets	(32)	1,543
Other non-current assets	(3,184)
Accounts payable	1,247	(2,503)
Accrued and other current liabilities	585	(2,968)
Operating lease liabilities	(1,748)	(1,350)
Net cash used in operating activities	(81,991)	(97,665)
Investing activities:
Purchases of property and equipment	(9)	(186)
Purchases of available-for-sale securities	(411,900)	(83,612)
Proceeds from maturities of available-for-sale securities	192,100	156,684
Net cash (used in) provided by investing activities	(219,809)	72,886
Financing activities:
Proceeds from the exercise of common stock options	918	111
Proceeds from Employee Stock Purchase Plan purchases	215	345
Proceeds from the issuance of common stock, including related party of zero and $17,995 for the nine months ended September 30, 2024 and 2023, respectively	39,737	17,995
Proceeds from the issuance of common stock and pre-funded warrants, net of commissions	117,500
Payment of financing costs	(2,131)	(525)
Net cash provided by financing activities	156,239	17,926
Decrease in cash, cash equivalents and restricted cash	(145,561)	(6,853)
Effect of exchange rate changes on cash, cash equivalents and restricted cash	(9)	(8)
Cash, cash equivalents and restricted cash
Beginning of period	226,142	141,052
End of period	80,572	134,191
Supplemental disclosure of cash flow information:
Cash paid for amounts included in the measurement of lease liability	3,649	3,525
Non-cash investing and financing activities:
Deferred offering costs included in accounts payable and accrued liabilities	14
Deferred offering costs included in other non-current assets	$ 49
Purchases of property and equipment included in accounts payable and accrued liabilities		$ 6

Net Loss Per Share - Summary of Outstanding Potentially Dilutive Shares Excluded From Calculation of Diluted Net Loss Per Share (Detail) - shares	3 Months Ended		9 Months Ended
	Sep. 30, 2024	Sep. 30, 2023	Sep. 30, 2024	Sep. 30, 2023
Antidilutive Securities Excluded From Computation Of Earnings Per Share [Line Items]
Anti-dilutive securities excluded from the computation of diluted net loss per share	21,681,372	18,394,507	21,681,372	18,394,507
Shares Subject to Employee Stock Purchase Plan [Member]
Antidilutive Securities Excluded From Computation Of Earnings Per Share [Line Items]
Anti-dilutive securities excluded from the computation of diluted net loss per share	36,364	97,880	36,364	97,880
Stock Options to Purchase Common Stock [Member]
Antidilutive Securities Excluded From Computation Of Earnings Per Share [Line Items]
Anti-dilutive securities excluded from the computation of diluted net loss per share	12,757,684	9,335,202	12,757,684	9,335,202
Unvested Restricted Stock Units [Member]
Antidilutive Securities Excluded From Computation Of Earnings Per Share [Line Items]
Anti-dilutive securities excluded from the computation of diluted net loss per share	782,709	533,917	782,709	533,917
Common Warrants [Member]
Antidilutive Securities Excluded From Computation Of Earnings Per Share [Line Items]
Anti-dilutive securities excluded from the computation of diluted net loss per share	8,104,615	8,427,508	8,104,615	8,427,508

Stockholder's Equity - Additional Information (Detail) - USD ($) $ / shares in Units, $ in Thousands	1 Months Ended									3 Months Ended					9 Months Ended
	Nov. 14, 2024	Jun. 30, 2024	Apr. 30, 2024	Mar. 31, 2024	Feb. 29, 2024	Dec. 31, 2023	Mar. 31, 2023	Jul. 31, 2022	Aug. 31, 2021	Sep. 30, 2024	Jun. 30, 2024	Mar. 31, 2024	Jun. 30, 2023	Mar. 31, 2023	Sep. 30, 2024	Sep. 30, 2023
Class Of Stock [Line Items]
Net proceeds from private placement								$ 122,500
Share option expired															248,907
Common stock						$ 78				$ 106					$ 106
Net proceeds from sale of common stock															$ 39,737	$ 17,995
Common Stock [Member]
Class Of Stock [Line Items]
Sale of shares											936,719	6,639,348
Common stock shares issued for exercise of warrants		19,901	965,427		5,243,400		2,582,557
Share option expired										107,467	35,914	105,526	283	55,605
Common Stock [Member] \| Subsequent Event [Member]
Class Of Stock [Line Items]
Common stock shares issued for exercise of warrants	2,739,096
Pre-funded Warrants [Member]
Class Of Stock [Line Items]
Purchase of shares		7,000,000				18,379,861					7,000,000
Offering price per share		$ 6.249				$ 2.879		$ 3.87025
Pre-funded warrants were recorded at fair value		$ 43,700				$ 52,900
Pre-funded Warrants [Member] \| Maximum [Member]
Class Of Stock [Line Items]
Purchase of shares								24,696,206
Purchase price per share		$ 0.001				$ 0.001		$ 0.001			$ 0.001
Warrants or Common Warrants [Member]
Class Of Stock [Line Items]
Offering price per share								3.87125
Purchase price per share								$ 5.806875
Warrant expiration date								Jun. 30, 2025
Warrants or Common Warrants [Member] \| Maximum [Member]
Class Of Stock [Line Items]
Purchase of shares								8,427,508
Private Placement [Member]
Class Of Stock [Line Items]
Sale of shares								9,013,834
Underwriting agreement [Member]
Class Of Stock [Line Items]
Sale of shares		13,001,120				25,035,000
Common stock, par value per share		$ 0.001				$ 0.001					0.001
Exchange value						$ 1,000
Shares issued price per share		$ 6.25				$ 2.88					$ 6.25
Net proceeds from sale of common stock		$ 116,800				$ 117,000
Underwriting agreement [Member] \| Director [Member]
Class Of Stock [Line Items]
Sale of shares						350,000
Sales Agreement with Cowen and Company LLC [Member] \| 2021 ATM Program [Member]
Class Of Stock [Line Items]
Common stock									$ 100,000
Percentage of gross proceeds of common stock to be paid									3.00%
Common stock, shares issued										7,576,067					7,576,067	2,646,458
Net proceeds from sale of common stock															$ 38,400	$ 17,500
Common stock sales agreement expiration date									Aug. 15, 2024
Number of common stock sold after expiration date									0
Sales Agreement with Cowen and Company LLC [Member] \| 2024 ATM Program [Member]
Class Of Stock [Line Items]
Common stock				$ 100,000								$ 100,000
Common stock, shares issued										0					0
Sales Agreement with Cowen and Company LLC [Member] \| 2024 ATM Program [Member] \| Maximum [Member]
Class Of Stock [Line Items]
Percentage of gross proceeds of common stock to be paid				3.00%
Sales Agreement with Cowen and Company LLC [Member] \| 2024 ATM Program [Member] \| Common Stock [Member] \| Subsequent Event [Member]
Class Of Stock [Line Items]
Sale of shares	750,000
Net proceeds from sale of common stock	$ 4,500

Balance Sheet Components - Summary of Accrued and Other Current Liabilities (Detail) - USD ($) $ in Thousands	Sep. 30, 2024	Dec. 31, 2023
Accrued Liabilities, Current [Abstract]
Accrued research and development expenses	$ 4,704	$ 4,027
Accrued compensation	4,389	5,607
Accrued professional services	1,562	501
Other accrued and current liabilities	206	141
Total accrued and other current liabilities	$ 10,861	$ 10,276

Condensed Consolidated Balance Sheets - USD ($) $ in Thousands	Sep. 30, 2024	Dec. 31, 2023
Current assets:
Cash and cash equivalents	$ 79,540	$ 225,110
Short-term investments	260,576	34,606
Prepaid expenses and other current assets	4,176	4,144
Total current assets	344,292	263,860
Restricted cash	1,032	1,032
Property and equipment, net	13,169	14,773
Operating lease right-of-use assets	17,050	18,009
Other non-current assets	3,233
Total assets	378,776	297,674
Current liabilities:
Accounts payable	6,748	5,487
Accrued and other current liabilities	10,861	10,276
Operating lease liabilities, current	2,437	2,165
Total current liabilities	20,046	17,928
Operating lease liabilities, non-current	27,170	29,190
Total liabilities	47,216	47,118
Commitments and contingencies (Note 5)
Stockholders’ equity:
Common stock	106	78
Additional paid-in capital	993,486	823,029
Accumulated other comprehensive loss	77	(52)
Accumulated deficit	(662,109)	(572,499)
Total stockholders’ equity	331,560	250,556
Total liabilities and stockholders’ equity	$ 378,776	$ 297,674

Equity Incentive Plans - Summary of Fair Value of Each Award Issued Estimated on the Date of Grant Using the Black-Scholes Option Pricing Model (Detail)	3 Months Ended		9 Months Ended
	Sep. 30, 2024	Sep. 30, 2023	Sep. 30, 2024	Sep. 30, 2023
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Expected term (in years)		6 years 29 days
Expected volatility, Minimum	96.80%	81.80%	95.90%	81.20%
Expected volatility, Maximum	97.60%	81.90%	97.80%	82.40%
Risk-free interest rate, Minimum	3.48%	4.20%	3.48%	3.47%
Risk-free interest rate, Maximum	4.15%	4.42%	4.65%	4.42%
Minimum [Member]
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Expected term (in years)	6 years 7 days		6 years 7 days	5 years 6 months
Maximum [Member]
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Expected term (in years)	6 years 29 days		6 years 29 days	6 years 29 days

- Definition

Line items represent financial concepts included in a table. These concepts are used to disclose reportable information associated with domain members defined in one or many axes to the table.

+ References

+ Details

Stockholder's Equity - Schedule of Common Stock Reserved for Future Issuance (Detail) - shares	Sep. 30, 2024	Dec. 31, 2023
Class Of Stock [Line Items]
Common stock reserved	12,757,684	9,208,970
Common stock reserved	2,059,871
Common stock reserved	94,410,198	65,329,843
Employee Stock Option [Member]
Class Of Stock [Line Items]
Common stock reserved	12,757,684	9,208,970
Stock Options Reserved for 2020 Incentive Award Plan [Member]
Class Of Stock [Line Items]
Common stock reserved	2,059,871	1,988,340
Unvested Restricted Stock Units Outstanding [Member]
Class Of Stock [Line Items]
Common stock reserved	782,709	495,579
Common Stock Reserved for Employee Stock Purchase Plan [Member]
Class Of Stock [Line Items]
Common stock reserved	2,023,537	1,338,381
2022 Employment Inducement Award Plan [Member]
Class Of Stock [Line Items]
Common stock reserved	2,398,730	758,084
Pre-Funded Warrants [Member]
Class Of Stock [Line Items]
Common stock reserved	41,283,052	40,493,510
Common Warrants [Member]
Class Of Stock [Line Items]
Common stock reserved	8,104,615	8,427,508
2021 ATM Program [Member]
Class Of Stock [Line Items]
Common stock reserved		2,619,471
2024 ATM Program [Member]
Class Of Stock [Line Items]
Common stock reserved	25,000,000

Fair Value Measurements

9 Months Ended

Sep. 30, 2024

Fair Value Disclosures [Abstract]

Fair Value Measurements

3. Fair Value Measurements

The Company utilizes valuation techniques that maximize the use of observable inputs and minimize the use of unobservable inputs to the extent possible. The Company determines fair value based on assumptions that market participants would use in pricing an asset or liability in the principal or most advantageous market. When considering market participant assumptions in fair value measurements, the following fair value hierarchy distinguishes between observable and unobservable inputs, which are categorized in one of the following levels:

•

Level 1 Inputs: Unadjusted quoted prices in active markets for identical assets or liabilities accessible to the reporting entity at the measurement date.

•

Level 2 Inputs: Other than quoted prices included in Level 1 inputs that are observable for the asset or liability, either directly or indirectly, for substantially the full term of the asset or liability.

•

Level 3 Inputs: Unobservable inputs for the asset or liability used to measure fair value to the extent that observable inputs are not available, thereby allowing for situations in which there is little, if any, market activity for the asset or liability at measurement date.

On a recurring basis, the Company measures certain financial assets and liabilities at fair value. The following tables summarize the fair value of the Company’s financial assets measured at fair value on a recurring basis by level within the fair value hierarchy (in thousands):


		September 30, 2024
	Valuation Hierarchy	Amortized Cost		Gross Unrealized Holding Gains		Gross Unrealized Holding Losses			Aggregate Fair Value
Assets:
Cash equivalents:
Money market funds	Level 1	$	40,679	$	—	$	—		$	40,679
Government bonds	Level 2		28,906		—		—			28,906
Total cash equivalents			69,585		—		—			69,585
Short-term investments:
Government bonds	Level 2		260,421		158		(3	)		260,576
Total short-term investments			260,421		158		(3	)		260,576
		$	330,006	$	158	$	(3	)	$	330,161


		December 31, 2023
	Valuation Hierarchy	Amortized Cost		Gross Unrealized Holding Gains		Gross Unrealized Holding Losses		Aggregate Fair Value
Assets:
Cash equivalents:
Money market funds	Level 1	$	143,933	$	—	$	—	$	143,933
Government bonds	Level 2		72,689		—		—		72,689
Total cash equivalents			216,622		—		—		216,622
Short-term investments:
Government bonds	Level 2		34,596		10		—		34,606
Total short-term investments			34,596		10		—		34,606
		$	251,218	$	10	$	—	$	251,228

During the three and nine months ended September 30, 2024, the Company did not recognize any credit losses. The Company determined that the decline in fair value of debt securities was not due to credit-related factors, and no allowance for expected credit losses was recorded as of September 30, 2024. There were nominal unrealized losses as of September 30, 2024, and no unrealized losses have been in the loss position for more than 12 months. However, the Company is planning to hold these securities until maturity and expects to recover the amortized cost basis.

For the three and nine months ended September 30, 2024 and 2023, the Company recognized no material realized gains or losses on financial instruments.

- Definition

The entire disclosure for the fair value of financial instruments (as defined), including financial assets and financial liabilities (collectively, as defined), and the measurements of those instruments as well as disclosures related to the fair value of non-financial assets and liabilities. Such disclosures about the financial instruments, assets, and liabilities would include: (1) the fair value of the required items together with their carrying amounts (as appropriate); (2) for items for which it is not practicable to estimate fair value, disclosure would include: (a) information pertinent to estimating fair value (including, carrying amount, effective interest rate, and maturity, and (b) the reasons why it is not practicable to estimate fair value; (3) significant concentrations of credit risk including: (a) information about the activity, region, or economic characteristics identifying a concentration, (b) the maximum amount of loss the entity is exposed to based on the gross fair value of the related item, (c) policy for requiring collateral or other security and information as to accessing such collateral or security, and (d) the nature and brief description of such collateral or security; (4) quantitative information about market risks and how such risks are managed; (5) for items measured on both a recurring and nonrecurring basis information regarding the inputs used to develop the fair value measurement; and (6) for items presented in the financial statement for which fair value measurement is elected: (a) information necessary to understand the reasons for the election, (b) discussion of the effect of fair value changes on earnings, (c) a description of [similar groups] items for which the election is made and the relation thereof to the balance sheet, the aggregate carrying value of items included in the balance sheet that are not eligible for the election; (7) all other required (as defined) and desired information.

+ References

Reference 1: http://www.xbrl.org/2003/role/exampleRef
-Topic 820
-SubTopic 10
-Name Accounting Standards Codification
-Section 55
-Paragraph 107
-Publisher FASB
-URI https://asc.fasb.org/1943274/2147482078/820-10-55-107

Reference 2: http://www.xbrl.org/2003/role/exampleRef
-Topic 820
-SubTopic 10
-Name Accounting Standards Codification
-Section 55
-Paragraph 100
-Publisher FASB
-URI https://asc.fasb.org/1943274/2147482078/820-10-55-100

Reference 3: http://www.xbrl.org/2003/role/disclosureRef
-Topic 820
-SubTopic 10
-Name Accounting Standards Codification
-Section 50
-Paragraph 2
-Subparagraph (c)(3)
-Publisher FASB
-URI https://asc.fasb.org/1943274/2147482106/820-10-50-2

Reference 4: http://www.xbrl.org/2003/role/disclosureRef
-Topic 820
-SubTopic 10
-Name Accounting Standards Codification
-Section 50
-Paragraph 6A
-Subparagraph (a)
-Publisher FASB
-URI https://asc.fasb.org/1943274/2147482106/820-10-50-6A

Reference 5: http://www.xbrl.org/2003/role/disclosureRef
-Topic 820
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-Name Accounting Standards Codification
-Section 50
-Paragraph 2E
-Publisher FASB
-URI https://asc.fasb.org/1943274/2147482106/820-10-50-2E

Reference 6: http://www.xbrl.org/2003/role/disclosureRef
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-Paragraph 6A
-Subparagraph (h)
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Reference 10: http://www.xbrl.org/2003/role/disclosureRef
-Topic 820
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Reference 11: http://www.xbrl.org/2003/role/disclosureRef
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-Publisher FASB
-URI https://asc.fasb.org/1943274/2147478119/940-820-50-1

+ Details

Organization - Additional Information (Detail) - USD ($) $ in Thousands	Sep. 30, 2024	Dec. 31, 2023
Accounting Policies [Abstract]
Accumulated deficit	$ 662,109	$ 572,499
Cash and cash equivalents and short-term investments	$ 340,100

- Definition

Amount of accumulated undistributed earnings (deficit).

+ References + Details

Equity Incentive Plans - Additional Information (Detail) - USD ($)	3 Months Ended		9 Months Ended
	Sep. 30, 2024	Sep. 30, 2023	Sep. 30, 2024	Sep. 30, 2023	Mar. 31, 2024	Dec. 31, 2023	Jul. 31, 2022
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Percentage of number of shares of capital stock outstanding on last day of preceding year			4.00%
Stock option grants description			Awards granted under the 2020 Plan expire no later than ten years from the date of grant. For Incentive Stock Options, or ISOs, and Nonstatutory Stock Options, or NSOs, the option price shall not be less than 100% of the estimated fair value on the date of grant. Options granted typically vest over a four-year period but may be granted with different vesting terms.
Option expiry period			10 years
Vesting Period			4 years
Options available for future grant	2,059,871		2,059,871
Intrinsic value of options exercised	$ 200,000	$ 0	$ 500,000	$ 300,000
Weighted- average exercise price per share, Stock options granted			$ 5.7
Unrecognized stock-based compensation cost expected period for recognition			2 years 8 months 12 days
Common stock for future issuance	94,410,198		94,410,198			65,329,843
Total stock-based compensation expense	$ 4,609,000	4,549,000	$ 14,211,000	$ 13,816,000
Employees [Member]
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Weighted- average exercise price per share, Stock options granted			$ 4.51	$ 3.87
2022 Employment Inducement Award Plan [Member]
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Options available for future grant	2,398,730		2,398,730				4,850,000
Incentive Stock Options, or ISOs, and Nonstatutory Stock Options, or NSOs [Member] \| Minimum [Member]
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Purchase of Common stock at end of each offering period at price equal to percentage of fair market value of shares			100.00%
Employee Stock Option [Member]
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Unrecognized stock-based compensation cost	$ 28,300,000		$ 28,300,000
Restricted Stock Units [Member]
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Unrecognized stock-based compensation cost	$ 3,000,000		$ 3,000,000
Unrecognized stock-based compensation cost expected period for recognition			2 years
Employee Stock Purchase Plan [Member]
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Purchase of Common stock at end of each offering period at price equal to percentage of fair market value of shares			85.00%
Share purchases funded through payroll deductions minimum percentage of employee's eligible compensation					1.00%
Share purchases funded through payroll deductions maximum percentage of employee's eligible compensation	15.00%		15.00%
Common stock for future issuance	2,023,537		2,023,537			1,338,381
Percentage of shares of common stock outstanding on last day of immediately preceding fiscal year			1.00%
Total stock-based compensation expense	$ 16,000	$ 100,000	$ 100,000	$ 200,000

Equity Incentive Plans - Summary of Stock Option Activity (Detail) $ / shares in Units, $ in Thousands	9 Months Ended	12 Months Ended
	Sep. 30, 2024 USD ($) $ / shares shares	Dec. 31, 2023 USD ($) $ / shares shares
Share-Based Payment Arrangement [Abstract]
Number of shares, Beginning balance \| shares	9,208,970
Number of shares, Stock options granted \| shares	4,710,324
Number of shares, Stock options exercised \| shares	(248,907)
Number of shares, Stock options forfeited \| shares	(912,703)
Number of shares, Ending balance \| shares	12,757,684	9,208,970
Number of shares, Exercisable \| shares	6,429,000
Weighted- average exercise price per share, Beginning balance \| $ / shares	$ 10.31
Weighted- average exercise price per share, Stock options granted \| $ / shares	5.7
Weighted- average exercise price per share, Stock options exercised \| $ / shares	3.69
Weighted- average exercise price per share, Stock options forfeited \| $ / shares	10.96
Weighted- average exercise price per share, Ending balance \| $ / shares	8.69	$ 10.31
Weighted- average exercise price per share, Exercisable \| $ / shares	$ 11.22
Weighted- average remaining contractual term	7 years 9 months 14 days	7 years 6 months 10 days
Weighted- average remaining contractual term, Exercisable	6 years 6 months 18 days
Aggregate intrinsic value \| $	$ 8,435	$ 2,930
Aggregate intrinsic value, Exercisable \| $	$ 4,278

Condensed Consolidated Statements of Cash Flows (Parenthetical) - USD ($) $ in Thousands	9 Months Ended
	Sep. 30, 2024	Sep. 30, 2023
Net Cash Provided by (Used in) Financing Activities [Abstract]
Proceeds from the issuance of common stock including related party	$ 0	$ 17,995

Net Loss Per Share (Tables)

9 Months Ended

Sep. 30, 2024

Earnings Per Share [Abstract]

Summary of Outstanding Potentially Dilutive Shares Excluded From Calculation of Diluted Net Loss Per Share

The following outstanding potentially dilutive shares have been excluded from the calculation of diluted net loss per share due to their anti-dilutive effect:


	Three Months Ended September 30,				Nine Months Ended September 30,
	2024		2023		2024		2023
Stock options to purchase common stock		12,757,684		9,335,202		12,757,684		9,335,202
Shares subject to Employee Stock Purchase Plan		36,364		97,880		36,364		97,880
Unvested restricted stock units		782,709		533,917		782,709		533,917
Common warrants		8,104,615		8,427,508		8,104,615		8,427,508
Total		21,681,372		18,394,507		21,681,372		18,394,507

Basis of Presentation and Significant Accounting Policies (Policies)	9 Months Ended
	Sep. 30, 2024
Accounting Policies [Abstract]
Basis of Presentation	Basis of Presentation The accompanying unaudited condensed consolidated financial statements have been prepared in accordance with generally accepted accounting principles in the United States, or GAAP, and applicable rules and regulations of the SEC regarding interim financial reporting. The condensed consolidated balance sheet as of September 30, 2024, the condensed consolidated statements of operations, comprehensive loss, stockholders’ equity for the three and nine months ended September 30, 2024 and 2023 and the condensed consolidated statements of cash flows for the nine months ended September 30, 2024 and 2023 are unaudited. These unaudited condensed consolidated financial statements have been prepared on the same basis as the annual consolidated financial statements and, in the opinion of management, reflect all adjustments, which include only normal recurring adjustments, necessary to present fairly the Company’s consolidated financial position, results of operations and cash flows for the interim period presented. The financial data and the other financial information contained in these notes to the condensed consolidated financial statements related to the three-month periods are also unaudited. The results of operations for the three and nine months ended September 30, 2024 are not necessarily indicative of the results to be expected for the year ending December 31, 2024 or for any other future annual or interim period. The condensed consolidated balance sheet as of December 31, 2023 included herein was derived from the audited financial statements as of that date. These unaudited condensed consolidated financial statements should be read in conjunction with the Company's audited consolidated financial statements included in the Company’s Annual Report on Form 10-K for the year ended December 31, 2023, filed with the SEC on March 26, 2024.
Use of Estimates	Use of Estimates The preparation of financial statements in conformity with accounting principles generally accepted in the United States of America, or GAAP, requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities and disclosure of contingent assets and liabilities at the date of the financial statements and the reported expenses during the reporting period. Management evaluates its estimates, including but not limited to the fair value of investments, operating lease right-of-use assets and liabilities, valuation of deferred tax assets and uncertain tax positions (including valuation allowance), clinical trial accruals and stock-based compensation. The Company evaluates its estimates and assumptions on an ongoing basis using historical experience and other factors and adjusts those estimates and assumptions when facts and circumstances dictate. Actual results could differ from those estimates.
Principles of Consolidation	Principles of Consolidation The condensed consolidated financial statements include the operations of Annexon, Inc. and its wholly-owned subsidiary and include the results of operations and cash flows of these entities. All intercompany balances and transactions have been eliminated in consolidation.
Recently Issued Accounting Pronouncements	Recently Issued Accounting Pronouncements In November 2023, the Financial Accounting Standards Board (FASB) issued Accounting Standards Update (ASU) 2023-07, Segment Reporting: Improvements to Reportable Segment Disclosures, which requires disclosure of incremental segment information on an interim and annual basis. This ASU is effective for fiscal years beginning after December 15, 2023, and interim periods within fiscal periods beginning after December 15, 2024, and requires retrospective application to all prior periods presented in the financial statements. The Company adopted annual requirements under ASU 2023-07 on January 1, 2024 and plans to adopt interim requirements under ASU 2023-07 on January 1, 2025. The Company will begin including financial statement disclosures in accordance with ASU 2023-07 in its Annual Report on Form 10-K for the year ended December 31, 2024. The Company is evaluating the impact of this guidance on its financial statements and related disclosures. In December 2023, the FASB issued ASU 2023-09, Income Taxes: Improvements to Income Tax Disclosures, which requires enhanced annual disclosures regarding the rate reconciliation and income taxes paid information. ASU 2023-09 is effective for fiscal years beginning after December 15, 2024 and may be adopted on a prospective or retrospective basis. Early adoption is permitted. The Company is evaluating the impact of this guidance on its financial statements and related disclosures.

Balance Sheet Components - Schedule of Reconciliation of Cash, Cash Equivalents and Restricted Cash (Details) - USD ($) $ in Thousands	Sep. 30, 2024	Dec. 31, 2023
Cash, Cash Equivalents, Restricted Cash, and Restricted Cash Equivalents [Abstract]
Cash	$ 9,955	$ 8,488
Cash equivalents	69,585	216,622
Cash and cash equivalents	79,540	225,110
Restricted cash	1,032	1,032
Cash, cash equivalents and restricted cash	$ 80,572	$ 226,142

- Definition

Amount of currency on hand as well as demand deposits with banks or financial institutions. Includes other kinds of accounts that have the general characteristics of demand deposits. Excludes cash and cash equivalents within disposal group and discontinued operation.

+ References + Details

Condensed Consolidated Statements of Stockholders' Equity - USD ($) $ in Thousands	Total	Related Party [Member]	Common Stock [Member]	Common Stock [Member] Related Party [Member]	Additional Paid-in Capital [Member]	Additional Paid-in Capital [Member] Related Party [Member]	Accumulated Other Comprehensive Loss [Member]	Accumulated Deficit [Member]
Beginning Balance, Values at Dec. 31, 2022	$ 231,194		$ 48		$ 669,780		$ (372)	$ (438,262)
Beginning Balance, Shares at Dec. 31, 2022			47,722,995
Exercise of stock options	111				111
Exercise of stock options, Shares			55,605
Exercise of pre-funded warrants, Value			$ 3		(3)
Exercise of pre-funded warrants, Shares			2,582,557
Issuance of common stock, net of issuance costs, Value		$ 17,470		$ 2		$ 17,468
Issuance of common stock, net of issuance costs, Shares				2,646,458
Restricted stock vested in the period			73,058
Stock-based compensation	4,607				4,607
Other comprehensive income (loss)	155						155
Net loss	(38,676)							(38,676)
Ending Balance, Values at Mar. 31, 2023	214,861		$ 53		691,963		(217)	(476,938)
Ending Balance, Shares at Mar. 31, 2023			53,080,673
Beginning Balance, Values at Dec. 31, 2022	231,194		$ 48		669,780		(372)	(438,262)
Beginning Balance, Shares at Dec. 31, 2022			47,722,995
Net loss	(106,346)
Ending Balance, Values at Sep. 30, 2023	156,839		$ 53		701,517		(123)	(544,608)
Ending Balance, Shares at Sep. 30, 2023			53,238,985
Beginning Balance, Values at Mar. 31, 2023	214,861		$ 53		691,963		(217)	(476,938)
Beginning Balance, Shares at Mar. 31, 2023			53,080,673
Exercise of stock options, Shares			283
Issuance of common stock per Employee Stock Purchase Plan purchase , Shares			70,155
Issuance of common stock per Employee Stock Purchase Plan purchase , Value	345				345
Stock-based compensation	4,660				4,660
Other comprehensive income (loss)	46						46
Net loss	(35,188)							(35,188)
Ending Balance, Values at Jun. 30, 2023	184,724		$ 53		696,968		(171)	(512,126)
Ending Balance, Shares at Jun. 30, 2023			53,151,111
Restricted stock vested in the period			87,874
Stock-based compensation	4,549				4,549
Other comprehensive income (loss)	48						48
Net loss	(32,482)							(32,482)
Ending Balance, Values at Sep. 30, 2023	156,839		$ 53		701,517		(123)	(544,608)
Ending Balance, Shares at Sep. 30, 2023			53,238,985
Beginning Balance, Values at Dec. 31, 2023	250,556		$ 78		823,029		(52)	(572,499)
Beginning Balance, Shares at Dec. 31, 2023			78,369,099
Exercise of stock options	217				217
Exercise of stock options, Shares			105,526
Exercise of pre-funded warrants, Value			$ 5		(5)
Exercise of pre-funded warrants, Shares			5,243,400
Issuance of common stock, net of issuance costs, Value	32,198		$ 7		32,191
Issuance of common stock, net of issuance costs, Shares			6,639,348
Restricted stock vested in the period			124,695
Stock-based compensation	4,660				4,660
Other comprehensive income (loss)	(50)						(50)
Net loss	(25,176)							(25,176)
Ending Balance, Values at Mar. 31, 2024	262,405		$ 90		860,092		(102)	(597,675)
Ending Balance, Shares at Mar. 31, 2024			90,482,068
Beginning Balance, Values at Dec. 31, 2023	$ 250,556		$ 78		823,029		(52)	(572,499)
Beginning Balance, Shares at Dec. 31, 2023			78,369,099
Exercise of stock options, Shares	248,907
Net loss	$ (89,610)
Ending Balance, Values at Sep. 30, 2024	331,560		$ 106		993,486		77	(662,109)
Ending Balance, Shares at Sep. 30, 2024			105,710,290
Beginning Balance, Values at Mar. 31, 2024	262,405		$ 90		860,092		(102)	(597,675)
Beginning Balance, Shares at Mar. 31, 2024			90,482,068
Exercise of stock options	171				171
Exercise of stock options, Shares			35,914
Exercise of pre-funded warrants, Value			$ 1		(1)
Exercise of pre-funded warrants, Shares			965,427
Exercise of common warrants , Shares			19,901
Issuance of common stock, net of issuance costs, Value	6,126		$ 1		6,125
Issuance of common stock per Employee Stock Purchase Plan purchase , Shares			98,534
Issuance of common stock and pre-funded warrants, net of issuance costs of $8,183, Value	116,817		$ 13		116,804
Issuance of common stock and pre-funded warrants, net of issuance costs of $8,183, Shares			13,001,120
Issuance of common stock, net of issuance costs, Shares			936,719
Issuance of common stock per Employee Stock Purchase Plan purchase , Value	215		$ 1		214
Stock-based compensation	4,942				4,942
Other comprehensive income (loss)	13						13
Net loss	(29,610)							(29,610)
Ending Balance, Values at Jun. 30, 2024	361,079		$ 106		988,347		(89)	(627,285)
Ending Balance, Shares at Jun. 30, 2024			105,539,683
Exercise of stock options	530				530
Exercise of stock options, Shares			107,467
Restricted stock vested in the period			63,140
Stock-based compensation	4,609				4,609
Other comprehensive income (loss)	166						166
Net loss	(34,824)							(34,824)
Ending Balance, Values at Sep. 30, 2024	$ 331,560		$ 106		$ 993,486		$ 77	$ (662,109)
Ending Balance, Shares at Sep. 30, 2024			105,710,290

Insider Trading Arrangements	3 Months Ended
Insider Trading Arrangements	Sep. 30, 2024
Trading Arrangements, by Individual
Rule 10b5-1 Arrangement Adopted	false
Non-Rule 10b5-1 Arrangement Adopted	false
Rule 10b5-1 Arrangement Terminated	false
Non-Rule 10b5-1 Arrangement Terminated	false

Equity Incentive Plans

9 Months Ended

Sep. 30, 2024

Share-Based Payment Arrangement [Abstract]

Equity Incentive Plans

7. Equity Incentive Plans

In July 2020, the Company’s board of directors and stockholders adopted and approved the 2020 Incentive Award Plan, or the 2020 Plan, and the Employee Stock Purchase Plan, or the ESPP, which became effective in connection with the Company’s initial public offering, or the IPO.

The Company may not grant any additional awards under the 2011 Equity Incentive Plan, or the 2011 Plan. The 2011 Plan will continue to govern outstanding equity awards granted thereunder.

2020 Equity Incentive Plan

The number of shares of common stock reserved for issuance under the 2020 Plan automatically increases on the first day of January, in an amount equal to 4% of the total number of shares of the Company’s capital stock outstanding on the last day of the preceding year, or a lesser number of shares determined by the Company’s board of directors.

Awards granted under the 2020 Plan expire no later than ten years from the date of grant. For Incentive Stock Options, or ISOs, and Nonstatutory Stock Options, or NSOs, the option price shall not be less than 100% of the estimated fair value on the date of grant. Options granted typically vest over a four-year period but may be granted with different vesting terms. As of September 30, 2024, there were 2,059,871 shares available for issuance under the 2020 Plan.

2022 Employment Inducement Award Plan

In July 2022, the Company’s board of directors adopted the Annexon, Inc. 2022 Employment Inducement Award Plan, or, as amended, the Inducement Plan, and together with the 2011 Plan and the 2020 Plan, the Plans. The Inducement Plan was adopted by the Company’s board of directors without stockholder approval pursuant to Nasdaq Marketplace Rule 5635(c)(4), or Rule 5635(c)(4). In accordance with Rule 5635(c)(4), awards made under the Inducement Plan may only be granted to newly hired employees as an inducement material to the employees entering into employment with the Company. Awards granted under the Inducement Plan expire no later than ten years from the date of grant. An aggregate of 4,850,000 shares of common stock were reserved for issuance under the Inducement Plan. As of September 30, 2024, there were 2,398,730 shares available for issuance under the Inducement Plan.

Stock Options

The following table presents stock option activity under the Plans for the period:


	Number of Shares			Weighted- Average Exercise Price Per Share		Weighted- Average Remaining Contractual Term (in years)		Aggregate Intrinsic Value (in thousands)
Balances as of December 31, 2023		9,208,970		$	10.31		7.53	$	2,930
Stock options granted		4,710,324		$	5.70
Stock options exercised		(248,907	)	$	3.69
Stock options forfeited		(912,703	)	$	10.96
Balances as of September 30, 2024		12,757,684		$	8.69		7.79	$	8,435
Exercisable as of September 30, 2024		6,429,000		$	11.22		6.55	$	4,278

The total intrinsic value of options exercised was $0.2 million and zero for the three months ended September 30, 2024 and 2023, respectively, and $0.5 million and $0.3 million for the nine months ended September 30, 2024 and 2023, respectively. The intrinsic value is the difference between the fair value of the Company’s common stock at the time of exercise and the exercise price of the stock option.

The weighted-average grant date fair value of options granted to employees during the nine months ended September 30, 2024 and 2023 was $4.51 and $3.87 per share, respectively.

As of September 30, 2024, the total unrecognized stock-based compensation cost related to outstanding unvested stock options was $28.3 million, which the Company expects to recognize over an estimated weighted-average period of 2.7 years.

Restricted Stock Units

RSUs are share awards that entitle the holder to receive freely tradeable shares of the Company’s common stock upon vesting. The RSUs cannot be transferred and the awards are subject to forfeiture if the holder’s employment terminates prior to the release of the vesting restrictions. The RSUs generally vest over a three-year period in equal amounts on an annual basis, provided the employee remains continuously employed with the Company. The fair value of the RSUs is equal to the closing price of the Company’s common stock on the grant date.

A summary of RSU activity under the Company’s equity incentive plan and related information is as follows:


	Number of Shares			Weighted-Average Grant Date Fair Value Per Share
Unvested as of December 31, 2023		495,579		$	5.69
Granted		602,600			5.13
Vested		(187,835	)		5.59
Cancelled		(127,635	)		5.29
Unvested as of September 30, 2024		782,709		$	5.35

As of September 30, 2024, unrecognized stock-based compensation expense related to outstanding unvested RSUs was $3.0 million, which is expected to be recognized over a weighted-average period of 2.0 years.

Employee Stock Purchase Plan

The ESPP enables eligible employees to purchase shares of the Company’s common stock at the end of each offering period at a price equal to 85% of the fair market value of the shares on the first business day or the last business day of the offering period, whichever is lower. Eligible employees generally include all employees. Share purchases are funded through payroll deductions of at least 1%, and up to 15% of an employee’s eligible compensation for each payroll period. The number of shares reserved for issuance under the ESPP increase automatically on the first day of each fiscal year, by a number equal to, 1% of the shares of common stock outstanding on the

last day of the immediately preceding fiscal year, or such number of shares determined by the Company’s board of directors. As of September 30, 2024, 2,023,537 shares were available for future purchase. The ESPP generally provides for six-month consecutive offering periods beginning on May 16 and November 16 of each year. The ESPP is a compensatory plan as defined by the authoritative guidance for stock compensation. As such, stock-based compensation expense has been recorded for the three and nine months ended September 30, 2024.

The stock-based compensation expense related to the ESPP was $16,000 and $0.1 million for the three months ended September 30, 2024 and 2023, respectively, and $0.1 million and $0.2 million for the nine months ended September 30, 2024 and 2023.

Stock-Based Compensation Expense

The total stock-based compensation expense recognized was as follows (in thousands):


	Three Months Ended September 30,				Nine Months Ended September 30,
	2024		2023		2024		2023
Research and development	$	2,325	$	2,243	$	6,918	$	6,801
General and administrative		2,284		2,306		7,293		7,015
Total stock-based compensation expense	$	4,609	$	4,549	$	14,211	$	13,816

To determine the value of stock option awards for stock-based compensation purposes, the Company uses the Black-Scholes option pricing model and the assumptions discussed below. Each of these inputs is subjective and generally requires significant judgment.

Fair Value of Common Stock—The fair value of each share of underlying common stock is based on the closing price of the Company’s common stock as reported on the date of grant on the Nasdaq Global Select Market.

Expected Term—The expected term represents the period that the stock-based awards are expected to be outstanding and is determined using the simplified method (based on the mid-point between the vesting date and the end of the contractual term). The Company continues using the simplified method as it does not have sufficient historical exercise data to provide a reasonable basis upon which to estimate expected term due to the limited period of time its equity shares have been publicly traded.

Expected Volatility—Beginning in 2024, the expected volatility was estimated based on a weighted volatility using both the Company’s trading history for its common stock and the average volatility for comparable publicly traded life sciences companies over a period equal to the expected term of the stock option grants. Prior to 2024, the expected volatility was estimated based on the average volatility for comparable publicly traded life sciences companies over a period equal to the expected term of the stock option grants. The comparable companies were chosen based on the similar size, stage in life cycle or area of specialty.

Risk-Free Interest Rate—The risk-free interest rate is based on the U.S. Treasury zero coupon issues in effect at the time of grant for periods corresponding with the expected term of the option.

Dividend Yield—The Company has never paid dividends on its common stock and has no plans to pay dividends on its common stock. Therefore, the Company used an expected dividend yield of zero.

The fair value of each stock option issued was estimated on the date of grant using the Black-Scholes option pricing model with the following assumptions:


	Three Months Ended September 30,		Nine Months Ended September 30,
	2024	2023	2024	2023
Expected term (in years)	6.02 - 6.08	6.08	6.02 - 6.08	5.50 - 6.08
Expected volatility	96.80% - 97.60%	81.80% - 81.90%	95.90% - 97.80%	81.20% - 82.40%
Risk-free interest rate	3.48% - 4.15%	4.20% - 4.42%	3.48% - 4.65%	3.47% - 4.42%
Dividend yield	—	—	—	—

Organization

9 Months Ended

Sep. 30, 2024

Accounting Policies [Abstract]

Organization

1. Organization

Annexon, Inc., or the Company, is a clinical-stage biopharmaceutical company pioneering a new class of complement medicines for people living with devasting inflammatory-related diseases. The Company is located in Brisbane, California and was incorporated in Delaware in March 2011.

The Company’s wholly-owned subsidiary, Annexon Biosciences Australia Pty Ltd, or the Subsidiary, is a proprietary limited company incorporated in 2016 and domiciled in Australia.

Liquidity

Since inception, the Company has been involved primarily in performing research and development activities, conducting clinical trials, hiring personnel, and raising capital to support and expand these activities. The Company has experienced losses and negative cash flows from operations since its inception and, as of September 30, 2024, had an accumulated deficit of $662.1 million and cash and cash equivalents and short-term investments of $340.1 million.

The Company has historically funded its operations through the issuance of shares of its common stock and warrants. Based on projected activities, management projects that existing cash and cash equivalents and short-term investments will enable the Company to fund its operating expenses and capital expenditure requirements for at least twelve months from the date of issuance of these financial statements. The Company’s future viability beyond that point is dependent on its ability to achieve development and regulatory milestones and obtain additional funding. Management expects to continue to incur losses and negative cash flows from operations for at least the next several years. There are uncertainties associated with the Company’s ability to (1) obtain additional equity or debt financing on terms that are favorable to the Company, (2) enter into collaborative agreements with strategic partners, and (3) succeed in its future operations. If the Company is not able to obtain the required funding for its operations or is not able to obtain funding on terms that are favorable to the Company, it could be forced to delay, reduce or eliminate its research and development programs and its business could be materially harmed.