SEC Filing | Alumis Inc.

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UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

FORM 10-Q

(Mark One)

☒QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES
EXCHANGE ACT OF 1934

For the quarterly period ended June 30, 2024

☐TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES
EXCHANGE ACT OF 1934

For the transition period from to

Commission File Number: 001-42143

Alumis Inc.

(Exact name of registrant as specified in its charter)


Delaware	86-1771129
(State or other jurisdiction of incorporation or organization)	(I.R.S. Employer Identification Number)

280 East Grand Avenue

South San Francisco, CA 94080

(Address of Principal Executive Offices)

(650) 231-6625

(Registrant’s telephone number)

Indicate by check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days. Yes ☐ No ☒

Indicate by check mark whether the registrant has submitted electronically every Interactive Data File required to be submitted pursuant to Rule 405 of Regulation S-T (§232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to submit such files). Yes ☒ No ☐

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, a smaller reporting company, or an emerging growth company. See the definitions of “large accelerated filer,” “accelerated filer,” “smaller reporting company,” and “emerging growth company” in Rule 12b-2 of the Exchange Act.


Large accelerated filer	☐	Accelerated filer	☐

Non-accelerated filer	☒	Smaller reporting company	☒	Emerging growth company	☒

If an emerging growth company, indicate by check mark if the registrant has elected not to use the extended transition period for complying with any new or revised financial accounting standards provided pursuant to Section 13(a) of the Exchange Act. ☐

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act). Yes ☐ No ☒

Securities registered pursuant to Section 12(b) of the Act:


Title of Each Class	Trading symbol	Name of Exchange on which registered
Common Stock, par value $0.0001 per share	ALMS	The Nasdaq Global Select Market

As of August 7, 2024, the registrant had 47,218,394 shares of common stock, $0.0001 par value per share, and 7,184,908 shares of non-voting common stock, $0.0001 par value per share, outstanding.

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TABLE OF CONTENTS

		Page

Part I	Financial Information

Item 1.	Financial Statements (Unaudited)	3

	Condensed Consolidated Balance Sheets	3

	Condensed Consolidated Statements of Operations and Comprehensive Loss	4

	Condensed Consolidated Statements of Redeemable Convertible Preferred Stock and Stockholders’ Deficit	5

	Condensed Consolidated Statements of Cash Flows	6

	Notes to Condensed Consolidated Financial Statements	7

Item 2.	Management’s Discussion and Analysis of Financial Condition and Results of Operations	31

Item 3.	Quantitative and Qualitative Disclosures about Market Risk	44

Item 4.	Controls and Procedures	45

Part II	Other Information

Item 1.	Legal Proceedings	46

Item 1A.	Risk Factors	46

Item 2.	Unregistered Sales of Equity Securities and Use of Proceeds	109

Item 3.	Defaults Upon Senior Securities	110

Item 4.	Mine Safety Disclosures	110

Item 5.	Other Information	110

Item 6.	Exhibits	111

Signatures		113

In this Quarterly Report on Form 10-Q, unless otherwise stated or as the context otherwise requires, references to “Alumis,” “the Company,” “we,” “us,” “our” and similar references refer to Alumis Inc.

This Quarterly Report on Form 10-Q also contains registered marks, trademarks and trade names of other companies. All other trademarks, registered marks and trade names appearing in this report are the property of their respective holders. We do not intend our use or display of other companies’ trade names, trademarks or service marks to imply a relationship with, or endorsement or sponsorship of us by, these other companies.

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SPECIAL NOTE REGARDING FORWARD-LOOKING STATEMENTS

This Quarterly Report on Form 10-Q contains forward-looking statements that are based on our management’s beliefs and assumptions and on information currently available to our management. All statements, other than statements of historical facts contained in this Quarterly Report on Form 10-Q, including statements regarding our future financial condition, business strategy and plans, and objectives of management for future operations, are forward-looking statements. In some cases, you can identify forward-looking statements by the following words: “anticipate,” “believe,” “continue,” “could,” “estimate,” “expect,” “intend,” “may,” “ongoing,” “plan,” “potential,” “predict,” “project,” “should,” “will,” “would” or the negative of these terms or other comparable terminology, although not all forward-looking statements contain these words.

These forward-looking statements involve risks, uncertainties and other factors that may cause our actual results, levels of activity, performance or achievements to be materially different from the information expressed or implied by these forward-looking statements. Although we believe that we have a reasonable basis for each forward-looking statement contained in this Quarterly Report on Form 10-Q, we caution you that these statements are based on a combination of facts and factors currently known by us and our projections of the future, about which we cannot be certain. Forward-looking statements in this Quarterly Report on Form 10-Q include, but are not limited to, statements about:

●	our expectations regarding the potential benefits of our strategy;

●	our expectations regarding the operation of our product candidates and related benefits;

●	the success of competing therapies that are, or may become, available;

●	developments relating to our competitors and our industry, including competing product candidates and therapies;

●	details regarding our strategic vision and planned product candidate pipeline;

●	our beliefs regarding the success, cost and timing of our product candidate development activities and current and future clinical trials and studies, including study design;

●	the timing or likelihood of regulatory filings or other actions and related regulatory authority responses;

●	the ability and willingness of various third parties to engage in research and development activities involving our product candidates, and our ability to leverage those activities;

●	our expectations regarding the ease of administration associated with our product candidates;

●	our expectations regarding the patient compatibility associated with our product candidates;

●	our beliefs regarding the potential markets for our product candidates and our ability to serve those markets;

●	the ability to obtain and maintain regulatory approval of any of our product candidates, and any related restrictions, limitations and/or warnings in the label of any approved product candidate;

●	our ability to commercialize any approved products;

●	the rate and degree of market acceptance of any approved products;

●	our ability to attract and retain key personnel;

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●	the accuracy of our estimates regarding our future revenue, as well as our future operating expenses, capital requirements and needs for additional financing;

●	our ability to obtain funding for our operations, including funding necessary to complete further development and any commercialization of our product candidates;

●	our ability to obtain, maintain, protect and enforce intellectual property protection for our product candidates and technology and not infringe, misappropriate or otherwise violate the intellectual property of others;

●	regulatory developments in the United States and foreign countries;

●	our expectations regarding the period during which we qualify as an “emerging growth company” under the JOBS Act, and a “smaller reporting company,” as defined in Rule 12b-2 of the Securities Exchange Act of 1934, as amended (the “Exchange Act”); and

●	statements of belief and any statement of assumptions underlying any of the foregoing.

You should refer to the section titled “Risk Factors” in Part II, Item 1A. of this Quarterly Report on Form 10-Q for a discussion of other important factors that may cause our actual results to differ materially from those expressed or implied by our forward-looking statements. As a result of these factors, we cannot assure you that the forward-looking statements in this Quarterly Report on Form 10-Q will prove to be accurate.

In addition, statements that “we believe” and similar statements reflect our beliefs and opinions on the relevant subject. These statements are based upon information available to us as of the date of this Quarterly Report on Form 10-Q, and although we believe such information forms a reasonable basis for such statements, such information may be limited or incomplete, and our statements should not be read to indicate that we have conducted a thorough inquiry into, or review of, all potentially available relevant information. These statements are inherently uncertain, and investors are cautioned not to unduly rely upon these statements.

Furthermore, if our forward-looking statements prove to be inaccurate, the inaccuracy may be material. In light of the significant uncertainties in these forward-looking statements, you should not regard these statements as a representation or warranty by us or any other person that we will achieve our objectives and plans in any specified time frame, or at all. We undertake no obligation to publicly update any forward-looking statements, whether as a result of new information, future events or otherwise, except as required by law.

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PART I—FINANCIAL INFORMATION

Item 1. Financial Statements (Unaudited)

ALUMIS INC.

CONDENSED CONSOLIDATED BALANCE SHEETS

(Unaudited)


	June 30,		December 31,
(in thousands, except share and per share amounts)	2024		2023
Assets
Current assets
Cash and cash equivalents	$	155,108	$	45,996
Restricted cash		113		113
Marketable securities		54,423		2,956
Research and development prepaid expenses		13,200		2,661
Other prepaid expenses and current assets		2,012		1,631
Total current assets		224,856		53,357
Restricted cash, non-current		1,024		1,024
Property and equipment, net		22,173		22,441
Operating lease right-of-use assets, net		12,772		12,783
Other long-term assets		4,354		7
Total assets	$	265,179	$	89,612
Liabilities, Redeemable Convertible Preferred Stock and Stockholders’ Deficit
Current liabilities
Accounts payable	$	9,188	$	1,118
Research and development accrued expenses		14,584		10,946
Other accrued expenses and current liabilities		8,118		7,087
Operating lease liabilities, current		1,523		1,720
Total current liabilities		33,413		20,871
Operating lease liabilities, non-current		30,050		30,860
Share repurchase liability		1,234		1,771
Total liabilities		64,697		53,502
Commitments and contingencies (Note 7)
Redeemable convertible preferred stock, $0.0001 par value; 202,643,727 and 89,016,578 shares authorized as of June 30, 2024 and December 31, 2023, respectively; 168,489,871 and 85,960,088 shares issued and outstanding as of June 30, 2024 and December 31, 2023, respectively; aggregate liquidation preference of $629,540 and $370,540 as of June 30, 2024 and December 31, 2023, respectively		639,237		375,370
Stockholders’ deficit:
Common stock, $0.0001 par value; 225,000,000 and 125,000,000 Class A shares authorized as of June 30, 2024 and December 31, 2023, respectively; 2,741,498 and 2,675,979 Class A shares issued and outstanding as of June 30, 2024 and December 31, 2023, respectively; 168,489,897 and 85,960,088 Class B shares authorized as of June 30, 2024 and December 31, 2023, respectively; no Class B shares issued and outstanding as of June 30, 2024 and December 31, 2023		1		1
Additional paid-in capital		31,920		25,055
Accumulated other comprehensive (loss) income		(1)		2
Accumulated deficit		(470,675)		(364,318)
Total stockholders’ deficit		(438,755)		(339,260)
Total liabilities, redeemable convertible preferred stock and stockholders’ deficit	$	265,179	$	89,612

The accompanying notes are an integral part of these condensed consolidated financial statements.

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ALUMIS INC.

CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS AND

COMPREHENSIVE LOSS

(Unaudited)


	Three Months Ended June 30,				Six Months Ended June 30,
(in thousands, except share and per share amounts)	2024		2023		2024		2023
Operating expenses:
Research and development expenses, including related party expenses of $213, $429, $571 and $754 for the three and six months ended June 30, 2024 and 2023, respectively	$	48,565	$	32,848	$	90,526	$	65,283
General and administrative expenses		7,575		4,775		13,207		9,000
Total operating expenses		56,140		37,623		103,733		74,283
Loss from operations		(56,140)		(37,623)		(103,733)		(74,283)
Other income (expense):
Interest income		1,977		913		2,831		1,558
Change in fair value of derivative liability		(2,311)		432		(5,406)		432
Other income (expenses), net		(34)		(11)		(49)		(23)
Total other income (expense), net		(368)		1,334		(2,624)		1,967
Net loss	$	(56,508)	$	(36,289)	$	(106,357)	$	(72,316)
Other comprehensive income (loss):
Unrealized gain (loss) on marketable securities, net		—		30		(3)		130
Net loss and other comprehensive loss	$	(56,508)	$	(36,259)	$	(106,360)	$	(72,186)
Net loss per share attributable to Class A common stockholders, basic and diluted	$	(23.10)	$	(17.13)	$	(44.17)	$	(35.14)
Weighted-average Class A common shares outstanding, basic and diluted		2,446,022		2,117,861		2,408,037		2,058,178

The accompanying notes are an integral part of these condensed consolidated financial statements.

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ALUMIS INC.

CONDENSED CONSOLIDATED STATEMENTS OF REDEEMABLE CONVERTIBLE PREFERRED STOCK AND STOCKHOLDERS’ DEFICIT

(Unaudited)


	Redeemable								Accumulated
	Convertible						Additional		Other				Total
	Preferred Stock			Common Stock			Paid-In		Comprehensive		Accumulated		Stockholders’
(in thousands, except share amounts)	Shares	Amount		Shares	Amount		Capital		Income (Loss)		Deficit		Deficit
Balance at December 31, 2023	85,960,088	$	375,370	2,675,979	$	1	$	25,055	$	2	$	(364,318)	$	(339,260)
Issuance of Series C redeemable convertible preferred stock in March 2024 for cash, net of derivative liability of $8,913 and issuance costs of $382	41,264,891		120,205	—		—		—		—		—		—
Issuance of common stock upon exercise of stock options and early exercise of stock options	—		—	3,186		—		29		—		—		29
Vesting of early exercised stock options	—		—	—		—		494		—		—		494
Vesting of restricted shares of common stock	—		—	—		—		6		—		—		6
Stock-based compensation expense	—		—	—		—		2,657		—		—		2,657
Other comprehensive loss, net	—		—	—		—		—		(3)		—		(3)
Net loss	—		—	—		—		—		—		(49,849)		(49,849)
Balance at March 31, 2024	127,224,979	$	495,575	2,679,165	$	1	$	28,241	$	(1)	$	(414,167)	$	(385,926)

Issuance of Series C redeemable convertible preferred stock for cash and settlement of the derivative liability of $14,319, net of issuance costs of $157	41,264,892		143,662	—		—		—		—		—		—
Issuance of common stock upon exercise of stock options and early exercise of stock options	—		—	62,333		—		287		—		—		287
Vesting of early exercised stock options	—		—	—		—		253		—		—		253
Vesting of restricted shares of common stock	—		—	—		—		6		—		—		6
Stock-based compensation expense	—		—	—		—		3,133		—		—		3,133
Net loss	—		—	—		—		—		—		(56,508)		(56,508)
Balance at June 30, 2024	168,489,871	$	639,237	2,741,498	$	1	$	31,920	$	(1)	$	(470,675)	$	(438,755)


	Redeemable								Accumulated
	Convertible						Additional		Other				Total
	Preferred Stock			Common Stock			Paid-In		Comprehensive		Accumulated		Stockholders’
(in thousands, except share amounts)	Shares	Amount		Shares	Amount		Capital		(Loss) Income		Deficit		Deficit
Balance at December 31, 2022	67,960,088	$	285,473	2,642,334	$	1	$	14,209	$	(127)	$	(209,325)	$	(195,242)
Vesting of early exercised stock options	—		—	—		—		694		—		—		694
Vesting of restricted shares of common stock	—		—	—		—		5		—		—		5
Repurchase of unvested common stock shares issued upon early exercised stock options	—		—	(13,369)		—		—		—		—		—
Stock-based compensation expense	—		—	—		—		1,831		—		—		1,831
Other comprehensive income, net	—		—	—		—		—		100		—		100
Net loss	—		—	—		—		—		—		(36,027)		(36,027)
Balance at March 31, 2023	67,960,088	$	285,473	2,628,965	$	1	$	16,739	$	(27)	$	(245,352)	$	(228,639)

Issuance of Series B-2 and Series B-2A redeemable convertible preferred stock for cash, net of $2,112 derivative liability and $208 issuance costs	10,722,340		51,290	—		—		—		—		—		—
Issuance of Series B-2A redeemable convertible preferred stock for cash	1,277,660		6,389	—		—		—		—		—		—
Issuance of common stock upon exercise of stock options and early exercise of stock options	—		—	18,395		—		71		—		—		71
Vesting of early exercised stock options	—		—	—		—		559		—		—		559
Vesting of restricted shares of common stock	—		—	—		—		6		—		—		6
Stock-based compensation expense	—		—	—		—		1,909		—		—		1,909
Other comprehensive income, net	—		—	—		—		—		30		—		30
Net loss	—		—	—		—		—		—		(36,289)		(36,289)
Balance at June 30, 2023	79,960,088	$	343,152	2,647,360	$	1	$	19,284	$	3	$	(281,641)	$	(262,353)

The accompanying notes are an integral part of these condensed consolidated financial statements.

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ALUMIS INC.

CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS

(Unaudited)


	Six Months Ended June 30,
(in thousands)	2024		2023
Cash flows from operating activities
Net loss	$	(106,357)	$	(72,316)
Adjustments to reconcile net loss to net cash used in operating activities:
Stock-based compensation		5,790		3,740
Non-cash lease expense		12		1,520
Depreciation and amortization		1,518		240
Net accretion of discounts on marketable securities		(507)		(470)
Loss on disposal of fixed assets		5		—
Change in fair value of derivative liability		5,406		(432)
Changes in operating assets and liabilities:
Research and development prepaid expenses		(10,540)		2,081
Other prepaid expenses and other assets		(382)		(157)
Accounts payable		7,788		666
Research and development accrued expenses		3,638		2,276
Other accrued expenses and current liabilities		(1,912)		(245)
Operating lease liabilities		(1,007)		95
Net cash used in operating activities		(96,548)		(63,002)
Cash flows from investing activities
Maturities of marketable securities		8,000		66,500
Purchases of marketable securities		(58,964)		(8,340)
Purchases of property and equipment		(587)		(1,120)
Net cash (used in) provided by investing activities		(51,551)		57,040
Cash flows from financing activities
Proceeds from issuance of redeemable convertible preferred stock and derivative liability, net of issuance costs		258,461		59,791
Proceeds from issuance of common stock upon exercise of stock options		537		171
Payments of deferred offering costs		(1,787)		—
Repurchase of unvested common stock shares issued upon early exercised stock options		—		(51)
Net cash provided by financing activities		257,211		59,911
Net increase in cash, cash equivalents and restricted cash		109,112		53,949
Cash, cash equivalents and restricted cash at beginning of period		47,133		26,954
Cash, cash equivalents and restricted cash at end of period	$	156,245	$	80,903
Supplemental disclosures:
Right-of-use assets obtained in exchange for operating lease liabilities	$	—	$	14,255
Property and equipment acquired through tenant improvement allowance	$	—	$	11,537
Vesting of early exercised stock options and unvested restricted shares of common stock	$	759	$	1,264
Purchases of property and equipment in other accrued expenses and current liabilities	$	716	$	411
Recognition of derivative liability upon issuance of redeemable convertible preferred stock	$	8,913	$	2,112
Settlement of derivative liability upon issuance of redeemable convertible preferred stock	$	(14,319)	$	—
Deferred offering costs in accounts payable and other accrued expenses and current liabilities	$	2,559	$	90
Reconciliation of cash, cash equivalents and restricted cash:
Cash and cash equivalents	$	155,108	$	79,560
Restricted cash		113		206
Restricted cash, non-current		1,024		1,137
Total cash, cash equivalents and restricted cash	$	156,245	$	80,903

The accompanying notes are an integral part of these condensed consolidated financial statements.

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ALUMIS INC.

NOTES TO THE CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

(Unaudited)

1.	Organization and Nature of the Business

Organization and Business

Alumis Inc. (the “Company”) is a clinical stage biopharmaceutical company focused on identifying, acquiring, and accelerating the development and commercialization of transformative medicines for autoimmune disorders. The Company leverages its proprietary precision data analytics platform, biological insights, and a team of experts with deep experience in precision medicine drug discovery, development, and immunology, to create medicines that significantly improve the lives of patients by replacing broad immunosuppression with targeted therapies.

The Company was founded on January 29, 2021 as a Delaware corporation under the name FL2021-001, Inc. FL2021-001, Inc.’s name was changed to Esker Therapeutics, Inc. on March 8, 2021 and to Alumis Inc. on January 6, 2022. The Company is headquartered in South San Francisco, California.

Reverse Stock Split

On June 19, 2024, the board of directors approved, and on June 20, 2024, the Company effected, a reverse stock split of the shares of the Company’s outstanding common stock at a ratio of 1-for-4.675 (the “Reverse Stock Split”). The number of authorized shares and par value per share were not adjusted as a result of the Reverse Stock Split. All references to shares, options to purchase common stock, share amounts, per share amount, and related information contained in the condensed consolidated financial statements have been retrospectively adjusted to reflect the effect of the Reverse Stock Split for all periods presented. The shares of common stock underlying outstanding stock options and other equity instruments were proportionately reduced and the respective exercise prices, if applicable, were proportionately increased in accordance with the terms of the agreements governing such securities. In addition, the conversion ratios for each series of the Company’s redeemable convertible preferred stock, which were automatically convertible into shares of common stock upon the closing of the Company’s initial public offering (the “IPO”) of common stock, were proportionally adjusted.

Initial Public Offering and Concurrent Private Placement

On June 28, 2024, the Company’s Registration Statement on Form S-1 for its IPO was declared effective, and on July 1, 2024, the Company completed its IPO, pursuant to which it issued and sold 13,125,000 shares of its common stock at $16.00 price per share to the public. Net proceeds from the IPO were approximately $193.2 million, after deducting underwriting discounts and commissions and other offering costs totaling approximately $16.8 million.

In connection with the IPO, an existing investor and a holder of more than 5% of the Company’s capital stock, purchased an additional 2,500,000 shares of the Company’s common stock at the IPO price per share for a total of $40.0 million in a private placement transaction (the “Concurrent Private Placement”). The closing of the Concurrent Private Placement was contingent on the closing of the IPO. The sale of such shares is not registered under the Securities Act of 1933, as amended (the “Securities Act”), and as such, the shares may not be offered or sold absent registration or an applicable exemption from registration. The shares sold in connection with the Concurrent Private Placement are subject to existing resale registration rights and are subject to a 180-day lock-up agreement with the underwriters in the IPO. The Concurrent Private Placement closed on July 17, 2024.

Immediately prior to the closing of the IPO on July 1, 2024, all of the shares of the Company’s redeemable convertible preferred stock then outstanding converted into 28,855,656 shares of Class A common stock and 7,184,908 shares of Class B common stock at a 1-for-4.675 conversion ratio (the “Preferred Stock Conversion”). All outstanding Class A common stock shares and all outstanding Class B common stock shares were redesignated immediately thereafter into the same number of shares of common stock and non-voting common stock, respectively (the “Common Stock Reclassification”).

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ALUMIS INC.

NOTES TO THE CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (Continued)

(unaudited)

1.	Organization and Nature of the Business (Continued)

Initial Public Offering and Concurrent Private Placement (Continued)

The condensed consolidated financial statements as of June 30, 2024, including share and per share amounts, do not give effect to the Preferred Stock Conversion, the Common Stock Reclassification, the IPO or the Concurrent Private Placement, as they occurred subsequent to June 30, 2024.

In connection with the closing of the Company’s IPO, the Company increased the authorized number of shares to 500,000,000 shares of common stock and 50,000,000 shares of preferred stock. The authorized number of common stock shares includes voting common stock of 492,815,092 shares and non-voting common stock of 7,184,908 shares.

Liquidity

The Company has incurred negative operating cash flows and significant losses from operations since its inception. For the three and six months ended June 30, 2024, the Company incurred net losses of $56.5 million and $106.4 million, respectively. Cash used in operating activities was $96.5 million and $63.0 million for the six months ended June 30, 2024 and 2023, respectively. As of June 30, 2024, the Company had an accumulated deficit of $470.7 million.

The Company has historically financed its operations primarily through issuance of common stock and redeemable convertible preferred stock and convertible promissory notes in private placements, and most recently, through an initial public offering and concurrent private placement. The Company expects to continue to incur substantial losses for the foreseeable future, and its ability to achieve and sustain profitability will depend on the successful development, approval, and commercialization of any product candidates it may develop, and on the achievement of sufficient revenue to support its cost structure. The Company may never achieve profitability and, unless and until it does, it will need to continue to raise additional capital. As of June 30, 2024, the Company had cash, cash equivalents and marketable securities of $209.5 million. In July 2024, in connection with the closing of the IPO and the Concurrent Private Placement, the Company received an additional $233.2 million in aggregate net cash proceeds, net of underwriting discounts and commissions and other offering costs. Management believes that its existing cash, cash equivalents and marketable securities together with the IPO and the Concurrent Private Placement proceeds will be sufficient to fund its current operating plan for at least the next 12 months from the date of issuance of these condensed consolidated financial statements.

Additional funds are necessary to maintain current operations and to continue research and development activities. The Company’s management plans to monitor expenses and may raise additional capital through a combination of public and private equity, debt financings, strategic alliances, and licensing arrangements. The Company’s ability to access capital when needed is not assured and, if capital is not available to the Company when, and in the amounts, needed, on the terms which are favorable, the Company could be required to delay, scale back, or abandon some or all of its development programs and other operations, which could materially harm the Company’s business, financial condition and results of operations.

2.	Summary of Significant Accounting Policies and Basis of Presentation

The significant accounting policies and estimates used in the preparation of the accompanying condensed consolidated financial statements are described in the Company’s audited consolidated financial statements for the year ended December 31, 2023 included in the Company’s final prospectus for its IPO filed pursuant to Rule 424(b)(4) under the Securities Act with the Securities and Exchange Commission (the “SEC”), on June 28, 2024 (the “Prospectus”). There have been no material changes in the Company’s significant accounting policies during the three months ended June 30, 2024.

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ALUMIS INC.

NOTES TO THE CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (Continued)

(unaudited)

2.Summary of Significant Accounting Policies and Basis of Presentation (Continued)

Basis of Presentation

The condensed consolidated financial statements and accompanying notes are unaudited and have been prepared in accordance with accounting principles generally accepted in the United States of America (“U.S. GAAP”) and applicable rules and regulations of the SEC regarding interim financial reporting and do not contain all information that is included in the annual financial statements and notes thereto of the company.

Prior to their dissolution, the Company’s condensed consolidated financial statements included the accounts of FronThera U.S. Holdings, Inc. and FronThera U.S. Pharmaceuticals LLC, two wholly owned subsidiaries, and all intercompany transactions were eliminated. FronThera U.S. Holdings, Inc. was dissolved on April 8, 2024 and FronThera U.S. Pharmaceuticals LLC was dissolved on March 14, 2024.

The condensed consolidated interim financial statements have been prepared on the same basis as the audited annual financial statements and, in the opinion of management, reflect all adjustments, which include only normal recurring adjustments necessary for the fair statement of the Company’s financial position as of June 30, 2024 and the results of its operations and its cash flows for the three and six months ended June 30, 2024 and 2023. The condensed balance sheet as of December 31, 2023 was derived from audited annual consolidated financial statements but does not include all disclosures required by U.S. GAAP. The results of operations for the three and six months ended June 30, 2024 are not necessarily indicative of the results of operations to be expected for the full year or for any other subsequent interim period.

Any reference in these notes to applicable guidance is meant to refer to the authoritative U.S. GAAP as found in the Accounting Standards Codification (“ASC”) and Accounting Standards Updates (“ASU”) of the Financial Accounting Standards Board (“FASB”).

Use of Estimates

The preparation of financial statements in conformity with U.S. GAAP requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities, the disclosure of contingent assets and liabilities at the date of the financial statements and the reported amounts of expenses during the reporting period. On an ongoing basis, the Company evaluates estimates and assumptions, including but not limited to those related to the fair value of its common and redeemable convertible preferred stock, the fair value of derivative liability, stock-based compensation expense, accruals for research and development expenses and the valuation of deferred tax assets. Management bases its estimates on historical experience and on various other assumptions that are believed to be reasonable under the circumstances, the results of which form the basis for making judgments about the carrying values of assets and liabilities that are not readily apparent from other sources. Actual results may differ materially from those estimates.

Segment and Geographical Information

The Company operates and manages its business as one reportable and operating segment, which is the business of developing medicines for autoimmune disorders. The chief executive officer, who is the chief operating decision maker, reviews financial information on an aggregate basis for purposes of allocating resources and evaluating financial performance. All of the Company’s long-lived assets are located in the United States.

Concentration of Credit Risk

Financial instruments which potentially subject the Company to concentration of credit risk consist primarily of cash, investments in marketable securities and restricted cash. The Company maintains bank deposits in federally insured financial institutions and these deposits exceed federally insured limits. To date, the Company has not experienced any losses on its deposits of cash and periodically evaluates the creditworthiness of its financial institutions.

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ALUMIS INC.

NOTES TO THE CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (Continued)

(unaudited)

2.Summary of Significant Accounting Policies and Basis of Presentation (Continued)

The Company also invests in money market funds and U.S. treasuries, which are subject to certain credit risks. The Company mitigates the risks by investing in high-grade instruments, limiting its exposure to any one issuer and monitoring the ongoing creditworthiness of the financial institutions and issuers. The Company has not experienced any loss of principal on its financial instruments.

Risks and Uncertainties

The Company is subject to certain risks and uncertainties, including, but not limited to, changes in any of the following areas that the Company believes could have a material adverse effect on the future financial position or results of operations: the Company’s ability to advance the development of its proprietary precision data analytics platform, timing and ability to advance its product candidates through preclinical and clinical development; costs and timelines associated with the manufacturing of clinical supplies; regulatory approval, market acceptance of, and reimbursement for, any product candidates the Company may develop; performance of third-party vendors; competition from pharmaceutical or other biotechnology companies with greater financial resources or expertise; protection of intellectual property; litigation or claims against the Company based on intellectual property or other factors; and its ability to attract and retain employees necessary to support its growth.

The Company’s business and operations may be affected by worldwide economic conditions, which may continue to be impacted by global macroeconomic challenges, such as the effects of the ongoing military conflicts in Ukraine, Israel, and the Middle East, tensions in U.S.-China relations, uncertainty in the markets, including disruptions in the banking industry, the COVID-19 pandemic and inflationary trends. Fiscal year 2023 was marked by significant market uncertainty and increasing inflationary pressures. These market dynamics continue into 2024, and these and similar adverse market conditions may negatively impact the Company’s business, financial position and results of operations.

Deferred Finance Issuance Costs

Deferred finance issuance costs, consisting of legal, accounting and other third-party fees directly relating to in-process equity financings or offerings are capitalized. The deferred finance issuance costs will be offset against offering proceeds upon the completion of the financing or the offering. In the event the financing or the offering is terminated or delayed, deferred finance issuance costs will be expensed immediately as a charge to general and administrative expenses in the condensed consolidated statements of operations and comprehensive loss. The Company had $4.3 million in deferred finance issuance costs capitalized and included in other long-term assets in its condensed consolidated balance sheet as of June 30, 2024, which will be reclassified to equity upon the closing of the IPO in the third quarter of 2024. There were no deferred finance issuance costs capitalized and included in other long-term assets in the condensed consolidated balance sheet as of December 31, 2023.

Recent Accounting Pronouncements

From time to time, new accounting pronouncements are issued by the FASB or other standard setting bodies and adopted by the Company as of the specified effective date. The Company qualifies as an “emerging growth company” as defined in the Jumpstart Our Business Startups Act of 2012, as amended (the “JOBS Act”), and has elected not to “opt out” of the extended transition related to complying with new or revised accounting standards, which means that when a standard is issued or revised and it has different application dates for public and nonpublic companies, the Company will adopt the new or revised standard at the time nonpublic companies adopt the new or revised standard and will do so until such time that the Company either (i) irrevocably elects to “opt out” of such extended transition period or (ii) no longer qualifies as an emerging growth company. The Company may choose to early adopt any new or revised accounting standards whenever such early adoption is permitted for nonpublic companies.

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ALUMIS INC.

NOTES TO THE CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (Continued)

(unaudited)

2.Summary of Significant Accounting Policies and Basis of Presentation (Continued)

Recently Issued and Not Yet Adopted Accounting Pronouncements

In November 2023, the FASB issued ASU 2023-07, Segment Reporting (Topic 280): Improvements to Reportable Segment Disclosures. This ASU requires public entities to disclose information about their reportable segments’ significant expenses and other segment items on an interim and annual basis. Public entities with a single reportable segment are required to apply the disclosure requirements in ASU 2023-07, as well as all existing segment disclosures and reconciliation requirements in ASC 280 on an interim and annual basis. ASU 2023-07 is effective for fiscal years beginning after December 15, 2023, and for interim periods within fiscal years beginning after December 15, 2024, with early adoption permitted. The Company is currently evaluating the impact of adopting ASU 2023-07 on its condensed consolidated financial statements.

In December 2023, the FASB issued ASU No. 2023-09, Income Taxes (Topic 740): Improvements to Income Tax Disclosures, which requires the disclosure of specific categories in the rate reconciliation and greater disaggregation for income taxes paid. This standard is effective for annual periods beginning after December 15, 2024 and should be adopted prospectively with the option to be adopted retrospectively. The Company is currently evaluating the impact of this standard on its disclosure in its condensed consolidated financial statements.

In March 2024, the FASB issued ASU No. 2024-02, Codification Improvements - Amendments to Remove References to the Concepts Statements. The amendments in ASU 2024-02 clarify and simplify references to certain concept statements within U.S. GAAP. ASU 2024-02 is effective for fiscal years beginning after December 15, 2024, with early application permitted. The Company is currently evaluating the impact of the adoption of this standard on its condensed consolidated financial statements.

3.	Fair Value Measurements

The Company discloses and recognizes the fair value of its assets and liabilities using a hierarchy that prioritizes the inputs to valuation techniques used to measure fair value. The guidance establishes three levels of the fair value hierarchy as follows:

Level 1—Quoted prices in active markets for identical assets or liabilities.

Level 2—Observable inputs other than Level 1 prices, such as quoted prices for similar assets or liabilities, quoted prices in markets that are not active, or other inputs that are observable or can be corroborated by observable market data for substantially the full term of the assets or liabilities.

Level 3—Unobservable inputs that are supported by little or no market activity and that are significant to the fair value of the assets or liabilities.

Assets and liabilities measured at fair value are classified in their entirety based on the lowest level of input that is significant to the fair value measurement. The Company’s assessment of the significance of a particular input to the fair value measurement in its entirety requires management to make judgments and consider factors specific to the asset or liability. The Company recognizes transfers into and out of levels within the fair value hierarchy in the period in which the actual event or change in circumstances that caused the transfer occurs.

The Company’s financial instruments consist of Level 1, Level 2 and Level 3 financial instruments. Changes in the ability to observe valuation inputs may result in a reclassification of levels of certain securities within the fair value hierarchy.

Level 1 financial instruments are comprised of money market funds and U.S. treasuries. Level 2 financial instruments are comprised of U.S. treasuries. Usually, short term marketable securities are considered Level 2 when their fair values are determined using inputs that are observable in the market or can be derived principally from or corroborated by observable market data such as pricing for similar securities, recently executed transactions, cash flow models with yield curves, and

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NOTES TO THE CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (Continued)

(unaudited)

3.Fair Value Measurements (Continued)

benchmark securities. In addition, Level 2 financial instruments are valued using comparisons to like-kind financial instruments and models that use readily observable market data as their basis. Level 3 financial instruments include derivative liabilities issued in May 2023 and settled in October 2023 in connection with the closing of the second tranche of the Series B-2 and B-2A redeemable convertible preferred stock financing, and issued in March 2024 and settled in May 2024 in connection with the closing of the second tranche of the Series C redeemable convertible preferred stock financing.

The following tables represent the Company’s fair value hierarchy for financial assets and liabilities measured at fair value on a recurring basis as of June 30, 2024 and December 31, 2023 (in thousands):


	Fair Value Measurements as of June 30, 2024
	Level 1		Level 2		Level 3		Total
Assets:
Cash equivalents
Money market funds	$	104,826	$	—	$	—	$	104,826
U.S. treasuries		42,072		—		—		42,072
Marketable securities
U.S. treasuries		27,006		27,417		—		54,423
Total assets	$	173,904	$	27,417	$	—	$	201,321


	Fair Value Measurements as of December 31, 2023
	Level 1		Level 2		Level 3		Total
Assets:
Cash equivalents
Money market funds	$	21,310	$	—	$	—	$	21,310
U.S. treasuries		2,000		—		—		2,000
Marketable securities
U.S. treasuries		1,958		998		—		2,956
Total assets	$	25,268	$	998	$	—	$	26,266

The derivative liability issued in May 2023 in connection with the closing of the second tranche of the Series B-2 and B-2A redeemable convertible preferred stock financing was a freestanding financial instrument and represented the Company’s obligation to issue additional shares of Series B-2 and B-2A redeemable convertible preferred stock at a fixed price upon the approval by the Company’s board of directors. In connection with the Series C redeemable convertible preferred stock financing in March 2024, the Company issued to investors two freestanding financial instruments: the Series C second tranche option liability and the put right option liability. The Company estimated their fair value using a Black-Scholes option pricing model weighted by the probability of occurring. The Company used the intrinsic value calculation to estimate the fair value of the Series C second tranche option liability and the put right option liability upon settlement. Significant estimates and assumptions impacting the derivative liability fair value included the probability of each option exercise, redeemable convertible preferred stock fair value, estimated stock volatility and the expected term.

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ALUMIS INC.

NOTES TO THE CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (Continued)

(unaudited)

3.Fair Value Measurements (Continued)

The following tables provide a range of assumptions used in the valuation of the derivative liabilities for the six months ended June 30, 2024 and 2023:


	Six Months Ended June 30,
	2024	2023
Expected term (in years)	0.16 – 0.36	0.26 – 0.41
Expected volatility	55.1% – 59.9%	67.63% – 83.25%
Risk-free interest rate	5.4% – 5.5%	5.23% – 5.44%
Expected dividend yield	0%	0%
Probability of event occurring	0% – 100%	30%

The following table provides a roll-forward of the fair value of the Company’s Level 3 financial instrument, the derivative liabilities, for the six months ended June 30, 2024 and 2023 (in thousands):


Balance as of January 1, 2024	$	—
Fair value upon issuance		8,913
Changes in fair value		5,406
Fair value upon settlement		(14,319)
Balance as of June 30, 2024	$	—


Balance as of January 1, 2023	$	—
Fair value upon issuance		2,112
Changes in fair value		(432)
Balance as of June 30, 2023	$	1,680

There were no transfers between Level 1, Level 2 or Level 3 categories for the three and six months ended June 30, 2024 and 2023.

4.	Marketable Securities

Marketable securities, which are classified as available-for-sale marketable securities, consisted of the following as of June 30, 2024 and December 31, 2023 (in thousands):


			Gross		Gross		Fair Value as of
	Amortized Cost		Unrealized		Unrealized		June 30,
	Basis		Gains		Losses		2024
Short-term marketable securities:
U.S. treasuries	$	54,424	$	—	$	(1)	$	54,423
Total short-term marketable securities	$	54,424	$	—	$	(1)	$	54,423


			Gross		Gross		Fair Value as of
	Amortized Cost		Unrealized		Unrealized		December 31,
	Basis		Gains		Losses		2023
Short-term marketable securities:
U.S. treasuries	$	2,954	$	2	$	—	$	2,956
Total short-term marketable securities	$	2,954	$	2	$	—	$	2,956

All marketable securities held as of June 30, 2024 and December 31, 2023, had contractual maturities of less than one year.

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NOTES TO THE CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (Continued)

(unaudited)

4.	Marketable Securities (Continued)

As of June 30, 2024 and December 31, 2023, no significant facts or circumstances were present to indicate a deterioration in the creditworthiness of the issuers of the marketable securities, and the Company has no requirement or intention to sell these securities before maturity or recovery of their amortized cost basis. The Company considered the current and expected future economic and market conditions and determined that its investments were not significantly impacted. For all securities with a fair value less than its amortized cost basis, the Company determined the decline in fair value below amortized cost basis to be immaterial and non-credit related, and therefore no allowance for losses has been recorded. During the three and six months ended June 30, 2024 and 2023, the Company did not recognize any impairment losses on its investments.

5.Balance Sheet Components

Other Prepaid Expenses and Current Assets