ALUMIS INC. 10-K

Item 8. Financial Statements and Supplementary Data ALUMIS INC. INDEX TO CONSOLIDATED FINANCIAL STATEMENTS ​ ​ Page Report of Independent Registered Public Accounting Firm (PCAOB ID 238 ) ​ ​ 119 Consolidated Balance Sheets ​ 120 Consolidated Statements of Operations and Comprehensive Loss ​ 121 Consolidated Statements of Redeemable Convertible Preferred Stock and Stockholders’ Equity (Deficit) ​ 122 Consolidated Statements of Cash Flows ​ 123 Notes to Consolidated Financial Statements ​ 124 ​ ​ 118 Table of Contents Report of Independent Registered Public Accounting Firm To the Board of Directors and Stockholders of Alumis Inc. Opinion on the Financial Statements We have audited the accompanying consolidated balance sheets of Alumis Inc. and its subsidiaries (the “Company”) as of December 31, 2025 and 2024, and the related consolidated statements of operations and comprehensive loss, of redeemable convertible preferred stock and stockholders’ equity (deficit) and of cash flows for the years then ended, including the related notes (collectively referred to as the “consolidated financial statements”). In our opinion, the consolidated financial statements present fairly, in all material respects, the financial position of the Company as of December 31, 2025 and 2024, and the results of its operations and its cash flows for the years then ended in conformity with accounting principles generally accepted in the United States of America. Basis for Opinion These consolidated financial statements are the responsibility of the Company’s management. Our responsibility is to express an opinion on the Company’s consolidated financial statements based on our audits. We are a public accounting firm registered with the Public Company Accounting Oversight Board (United States) (PCAOB) and are required to be independent with respect to the Company in accordance with the U.S. federal securities laws and the applicable rules and regulations of the Securities and Exchange Commission and the PCAOB. We conducted our audits of these consolidated financial statements in accordance with the standards of the PCAOB. Those standards require that we plan and perform the audits to obtain reasonable assurance about whether the consolidated financial statements are free of material misstatement, whether due to error or fraud. The Company is not required to have, nor were we engaged to perform, an audit of its internal control over financial reporting. As part of our audits we are required to obtain an understanding of internal control over financial reporting but not for the purpose of expressing an opinion on the effectiveness of the Company's internal control over financial reporting. Accordingly, we express no such opinion. Our audits included performing procedures to assess the risks of material misstatement of the consolidated financial statements, whether due to error or fraud, and performing procedures that respond to those risks. Such procedures included examining, on a test basis, evidence regarding the amounts and disclosures in the consolidated financial statements. Our audits also included evaluating the accounting principles used and significant estimates made by management, as well as evaluating the overall presentation of the consolidated financial statements. We believe that our audits provide a reasonable basis for our opinion. /s/ PricewaterhouseCoopers LLP San Jose, California March 19, 2026 We have served as the Company’s auditor since 2022. ​ 119 Table of Contents ALUMIS INC. CONSOLIDATED BALANCE SHEETS ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, ​ ​ ​ December 31, (in thousands, except share and per share amounts) ​ 2025 ​ 2024 Assets ​ ​ ​ ​ Current assets: ​ ​ ​ ​ Cash and cash equivalents ​ $ 89,670 ​ $ 169,526 Restricted cash ​ 82 ​ — Marketable securities ​ 218,831 ​ 118,737 Research and development prepaid expenses ​ 2,909 ​ 13,424 Other prepaid expenses and current assets ​ 6,740 ​ 4,501 Total current assets ​ 318,232 ​ 306,188 Restricted cash, non-current ​ 1,301 ​ 1,106 Property and equipment, net ​ 18,190 ​ 20,968 Intangible assets ​ ​ 50,959 ​ ​ — Operating lease right-of-use assets, net ​ 16,971 ​ 12,723 Other assets, non-current ​ 6,287 ​ 7 Total assets ​ $ 411,940 ​ $ 340,992 Liabilities and Stockholders’ Equity ​ ​ ​ ​ Current liabilities: ​ ​ ​ ​ Accounts payable ​ $ 10,106 ​ $ 9,624 Research and development accrued expenses ​ 34,781 ​ 29,149 Deferred revenue, current ​ ​ 1,458 ​ ​ — Other accrued expenses and current liabilities ​ 22,303 ​ 10,580 Operating lease liabilities, current ​ 4,670 ​ 1,557 Total current liabilities ​ 73,318 ​ 50,910 Operating lease liabilities, non-current ​ 32,244 ​ 29,165 Deferred revenue, non-current ​ ​ 2,611 ​ ​ — Deferred tax liability ​ ​ 2,140 ​ ​ — Share repurchase liability ​ ​ 123 ​ ​ 813 Other liabilities, non-current ​ 207 ​ — Total liabilities ​ 110,643 ​ 80,888 Commitments and contingencies (Note 9) ​ ​ ​ ​ Stockholders’ equity: ​ ​ ​ ​ Preferred stock, $ 0.0001 par value; 50,000,000 shares authorized, zero shares issued and outstanding as of December 31, 2025 and December 31, 2024 ​ ​ — ​ ​ — Common stock, voting, $ 0.0001 par value; 492,815,092 voting shares authorized as of December 31, 2025 and December 31, 2024; 99,084,365 and 47,222,419 voting shares issued and outstanding as of December 31, 2025 and December 31, 2024, respectively ​ 9 ​ 4 Common stock, non-voting, $ 0.0001 par value; 7,184,908 non-voting shares authorized as of December 31, 2025 and December 31, 2024; 5,622,408 and 7,184,908 non-voting shares issued and outstanding as of December 31, 2025 and December 31, 2024, respectively ​ ​ 1 ​ ​ 1 Additional paid-in capital ​ 1,202,975 ​ 918,610 Accumulated other comprehensive income (loss) ​ 188 ​ 40 Accumulated deficit ​ ( 901,876 ) ​ ( 658,551 ) Total stockholders’ equity ​ 301,297 ​ 260,104 Total liabilities and stockholders’ equity ​ $ 411,940 ​ $ 340,992 ​ The accompanying notes are an integral part of these consolidated financial statements. ​ 120 Table of Contents ALUMIS INC. CONSOLIDATED STATEMENTS OF OPERATIONS AND COMPREHENSIVE LOSS ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year Ended December 31, ​ (in thousands, except share and per share amounts) ​ ​ ​ 2025 ​ ​ ​ 2024 ​ Revenue: ​ ​ ​ ​ ​ ​ ​ License revenue ​ $ 17,389 ​ $ — ​ Collaboration revenue ​ ​ 6,661 ​ ​ — ​ Total revenue ​ ​ 24,050 ​ ​ — ​ Operating expenses: ​ ​ ​ ​ ​ ​ ​ Research and development expenses, including related party expenses of $ 1,144 and $ 912 for the years ended December 31, 2025 and 2024, respectively ​ ​ 385,998 ​ ​ 265,554 ​ General and administrative expenses ​ ​ 91,856 ​ ​ 35,200 ​ Total operating expenses ​ 477,854 ​ 300,754 ​ Loss from operations ​ ( 453,804 ) ​ ( 300,754 ) ​ Other income (expense): ​ ​ ​ ​ ​ Gain on bargain purchase ​ 187,907 ​ — ​ Interest income ​ 14,180 ​ 12,020 ​ Change in fair value of derivative liability ​ — ​ ( 5,406 ) ​ Other income (expenses), net ​ ( 169 ) ​ ( 93 ) ​ Total other income (expense), net ​ 201,918 ​ 6,521 ​ Net loss before income taxes ​ ​ ( 251,886 ) ​ ​ ( 294,233 ) ​ Income tax benefit ​ ​ 8,561 ​ ​ — ​ Net loss ​ $ ( 243,325 ) ​ $ ( 294,233 ) ​ Other comprehensive income (loss): ​ ​ ​ ​ ​ Unrealized gain (loss) on marketable securities, net ​ 148 ​ 38 ​ Total comprehensive loss ​ $ ( 243,177 ) ​ $ ( 294,195 ) ​ Net loss per share attributable to common stockholders, basic and diluted ​ $ ( 2.86 ) ​ $ ( 10.38 ) ​ Weighted-average shares of common stock outstanding, basic and diluted ​ 85,029,624 ​ 28,341,866 ​ ​ The accompanying notes are an integral part of these consolidated financial statements. ​ 121 Table of Contents ALUMIS INC. CONSOLIDATED STATEMENTS OF REDEEMABLE CONVERTIBLE PREFERRED STOCK AND STOCKHOLDERS’ EQUITY (DEFICIT) ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ 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 Equity (Deficit) Balance as of 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 offering costs of $ 382 41,264,891 ​ 120,205 ​ — ​ — ​ — ​ — ​ — ​ — Issuance of Series C redeemable convertible preferred stock in May 2024 for cash and settlement of the derivative liability of $ 14,319 , net of offering costs of $ 157 41,264,892 ​ 143,662 ​ — ​ — ​ — ​ — ​ — ​ — Issuance of voting common stock upon initial public offering, net of underwriting discounts and commissions and other offering costs of $ 16,684 — ​ — ​ 13,125,000 ​ 1 ​ 193,315 ​ — ​ — ​ 193,316 Issuance of voting common stock in private placement transaction — ​ — ​ 2,500,000 ​ — ​ 40,000 ​ — ​ — ​ 40,000 Conversion and redesignation of redeemable convertible preferred stock into 28,855,656 shares of voting common stock and 7,184,908 shares of non-voting common stock in connection with initial public offering ( 168,489,871 ) ​ ( 639,237 ) ​ 36,040,564 ​ 3 ​ 639,234 ​ — ​ — ​ 639,237 Issuance of common stock upon exercise of stock options and early exercise of stock options — ​ — ​ 72,201 ​ — ​ 375 ​ — ​ — ​ 375 Vesting of early exercised stock options — ​ — ​ — ​ — ​ 1,154 ​ — ​ — ​ 1,154 Vesting of restricted shares of common stock ​ — ​ ​ — ​ ​ — ​ ​ — ​ 20 ​ — ​ — ​ ​ 20 Repurchase of unvested early exercised restricted common stock ​ — ​ ​ — ​ ​ ( 6,417 ) ​ ​ — ​ — ​ — ​ — ​ ​ — Stock-based compensation expense ​ — ​ ​ — ​ ​ — ​ ​ — ​ 19,457 ​ — ​ — ​ ​ 19,457 Other comprehensive income (loss), net — ​ — ​ — ​ — ​ — ​ 38 ​ — ​ 38 Net loss — ​ — ​ — ​ — ​ — ​ — ​ ( 294,233 ) ​ ( 294,233 ) Balance as of December 31, 2024 — ​ — ​ 54,407,327 ​ 5 ​ 918,610 ​ 40 ​ ( 658,551 ) ​ 260,104 Issuance of common stock and equity awards in connection with the ACELYRIN merger — ​ — ​ 48,653,549 ​ 5 ​ 238,072 ​ — ​ — ​ 238,077 Issuance of common stock upon vesting of RSUs — ​ — ​ 1,201,282 ​ — ​ — ​ — ​ — ​ — Issuance of common stock under the 2024 ESPP — ​ — ​ 388,739 ​ — ​ 1,595 ​ — ​ — ​ 1,595 Issuance of common stock upon exercise of stock options and early exercise of stock options — ​ — ​ 57,659 ​ — ​ 501 ​ — ​ — ​ 501 Vesting of early exercised stock options — ​ — ​ — ​ — ​ 671 ​ — ​ — ​ 671 Vesting of restricted shares of common stock — ​ — ​ — ​ — ​ 2 ​ — ​ — ​ 2 Repurchase of unvested early exercised stock options — ​ — ​ ( 1,783 ) ​ — ​ — ​ — ​ — ​ — Stock-based compensation expense — ​ — ​ — ​ — ​ 43,524 ​ — ​ — ​ 43,524 Other comprehensive income (loss), net — ​ — ​ — ​ — ​ — ​ 148 ​ — ​ 148 Net loss — ​ — ​ — ​ — ​ — ​ — ​ ( 243,325 ) ​ ( 243,325 ) Balance as of December 31, 2025 — ​ $ — ​ 104,706,773 ​ $ 10 ​ $ 1,202,975 ​ $ 188 ​ $ ( 901,876 ) ​ $ 301,297 ​ The accompanying notes are an integral part of these consolidated financial statements. ​ 122 Table of Contents ALUMIS INC. CONSOLIDATED STATEMENTS OF CASH FLOWS ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year Ended December 31, (in thousands) ​ 2025 ​ ​ ​ 2024 Cash flows from operating activities ​ ​ ​ ​ Net loss ​ $ ( 243,325 ) ​ $ ( 294,233 ) Adjustments to reconcile net loss to net cash used in operating activities: ​ ​ ​ ​ Stock-based compensation ​ 43,524 ​ 19,457 Net accretion of discounts on marketable securities ​ ( 5,298 ) ​ ( 3,685 ) Depreciation and amortization ​ 3,496 ​ 3,152 Non-cash lease expense ​ 1,701 ​ 60 Loss on disposal of fixed assets ​ — ​ 5 Change in fair value of derivative liability ​ — ​ 5,406 Gain on bargain purchase in connection with the ACELYRIN Merger ​ ​ ( 187,907 ) ​ ​ — Impairment of long-lived assets ​ ​ 529 ​ ​ — Changes in operating assets and liabilities: ​ ​ ​ ​ Research and development prepaid expenses ​ 11,473 ​ ( 10,763 ) Other prepaid expenses and other assets ​ 17,229 ​ ( 2,870 ) Other assets, non-current ​ ​ ( 5,535 ) ​ ​ — Accounts payable ​ ( 6,036 ) ​ 8,506 Deferred revenue ​ ​ 4,069 ​ ​ — Research and development accrued expenses ​ 2,087 ​ 18,203 Other accrued expenses and current liabilities ​ 6,036 ​ 3,542 Operating lease liabilities ​ ​ ( 3,212 ) ​ ​ ( 1,858 ) Other liabilities, non-current ​ ​ 207 ​ ​ — Deferred tax liability ​ ( 8,561 ) ​ — Net cash used in operating activities ​ ( 369,523 ) ​ ( 255,078 ) Cash flows from investing activities ​ ​ ​ ​ Maturities of marketable securities ​ 447,955 ​ 128,000 Purchases of marketable securities ​ ( 209,167 ) ​ ( 240,058 ) Purchases of property and equipment ​ ​ ( 653 ) ​ ​ ( 1,732 ) Cash, cash equivalents and restricted cash acquired in connection with the ACELYRIN Merger ​ 49,742 ​ — Net cash provided by (used in) investing activities ​ 287,877 ​ ( 113,790 ) Cash flows from financing activities ​ ​ ​ ​ Proceeds from issuance of redeemable convertible preferred stock and derivative liability, net of issuance costs ​ — ​ 258,461 Proceeds from initial public offering, net of underwriter discounts and commissions and other offering costs ​ ​ — ​ ​ 193,316 Proceeds from a private placement transaction ​ ​ — ​ ​ 40,000 Proceeds from issuance of common stock upon exercise of stock options ​ 489 ​ 596 Repurchase of common stock shares issued upon early exercised restricted common stock ​ ​ ( 17 ) ​ ​ ( 6 ) Proceeds from issuance of common stock under the 2024 ESPP ​ ​ 1,595 ​ ​ — Net cash provided by financing activities ​ 2,067 ​ 492,367 Net (decrease) increase in cash, cash equivalents and restricted cash ​ ( 79,579 ) ​ 123,499 Cash, cash equivalents and restricted cash at beginning of period ​ 170,632 ​ 47,133 Cash, cash equivalents and restricted cash at end of period ​ $ 91,053 ​ $ 170,632 Supplemental disclosures: ​ ​ ​ ​ Conversion of 168,489,871 shares of redeemable convertible preferred stock upon the closing of initial public offering ​ $ — ​ $ 639,237 Equity consideration transferred in connection with the ACELYRIN Merger ​ $ 238,077 ​ $ — Vesting of early exercised stock options and unvested restricted shares of common stock ​ $ 673 ​ $ 1,174 Right-of-use assets obtained in exchange for operating lease liabilities ​ $ 1,776 ​ $ — Recognition of derivative liability upon issuance of redeemable convertible preferred stock ​ $ — ​ $ 8,913 Settlement of derivative liability upon issuance of redeemable convertible preferred stock ​ $ — ​ $ ( 14,319 ) ​ ​ ​ ​ ​ ​ ​ Reconciliation of cash, cash equivalents and restricted cash: ​ ​ ​ ​ Cash and cash equivalents ​ $ 89,670 ​ $ 169,526 Restricted cash ​ 82 ​ — Restricted cash, non-current ​ 1,301 ​ 1,106 Total cash, cash equivalents and restricted cash ​ $ 91,053 ​ $ 170,632 ​ The accompanying notes are an integral part of these consolidated financial statements. ​ ​ 123 Table of Contents ALUMIS INC. NOTES TO CONSOLIDATED FINANCIAL STATEMENTS 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, in its mission 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. As of December 31, 2023, the Company had two wholly owned subsidiaries, FronThera U.S. Holdings, Inc. and FronThera U.S. Pharmaceuticals LLC. FronThera U.S. Holdings, Inc. was dissolved on April 8, 2024 and FronThera U.S. Pharmaceuticals LLC was dissolved on March 14, 2024. These subsidiaries did not have operations during the year ended December 31, 2024. As of December 31, 2025, the Company had two wholly owned subsidiaries, ACELYRIN, Inc. (“ACELYRIN”), a Delaware corporation incorporated on July 27, 2020 and its wholly owned subsidiary, WH2, LLC. Arrow Merger Sub, Inc. (“Merger Sub”), the Company’s wholly owned subsidiary incorporated in January 2025, was merged with and into ACELYRIN in May 2025. 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 amounts, and related information contained in the 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 IPO of common stock, were proportionally adjusted. IPO and Concurrent Private Placement 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 $ 193.3 million, after deducting underwriting discounts and commissions and other offering costs totaling $ 16.7 million. On July 17, 2024, 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 total gross and net proceeds of $ 40.0 million in the Concurrent Private Placement. 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 voting common stock and non-voting common stock, respectively. Unless the context otherwise requires a different meaning, all references to “common stock” in these notes refers to the Company’s voting common 124 Table of Contents ALUMIS INC. NOTES TO CONSOLIDATED FINANCIAL STATEMENTS stock and non-voting common stock combined. ACELYRIN Merger On February 6, 2025, the Company entered into an Agreement and Plan of Merger, and, on April 20, 2025, the Company entered into an Amendment to Agreement and Plan of Merger (collectively the “Merger Agreement”) with ACELYRIN and Merger Sub, a Delaware corporation and a direct wholly owned subsidiary of the Company. Under the terms of the Merger Agreement, Merger Sub merged with and into ACELYRIN, with ACELYRIN continuing as a direct wholly owned subsidiary of the Company (the “ACELYRIN Merger”). The Merger Agreement was approved by the disinterested directors on the Company’s board of directors and the board of directors of ACELYRIN and was approved by the stockholders of each company on May 13, 2025. On May 21, 2025, the Company completed the ACELYRIN Merger with ACELYRIN for a purchase consideration of approximately $ 238.1 million that included the issuance of 48,653,549 shares of the Company’s common stock and the fair value of replacement awards attributable to pre-combination services, to acquire net assets with a fair value of approximately $ 426.0 million. See Note 3 for additional information. Public Offering of Common Stock On January 7, 2026, the Company entered into the Underwriting Agreement with the Underwriters, relating to the issuance and sale in a public offering of 17,650,000 shares of the Company’s common stock at a price of $ 17.00 per share. In addition, the Company granted the Underwriters an option, exercisable for 30 days , to purchase up to 2,647,500 additional shares of common stock at the public offering price, less the underwriting discounts and commissions, which was exercised in full on January 8, 2026. On January 9, 2026, the offering closed and the Company received net proceeds of $ 324.4 million, after deducting underwriting discounts and commissions. The offering was made pursuant to a shelf registration statement on Form S-3 (File No. 333-288510) that was filed with the SEC on July 3, 2025 and declared effective by the SEC on August 19, 2025, and related prospectus and prospectus supplement thereunder. Liquidity The Company has incurred negative operating cash flows and significant losses from operations since its inception. For the years ended December 31, 2025 and 2024, the Company incurred net losses of $ 243.3 million and $ 294.2 million, respectively. Cash used in operating activities was $ 369.5 million and $ 255.1 million for the years ended December 31, 2025 and 2024, respectively. As of December 31, 2025, the Company had an accumulated deficit of $ 901.9 million. The Company has historically funded its operations primarily through the issuance of common stock, including in connection with the ACELYRIN Merger, its IPO and Concurrent Private Placement, the issuance of redeemable convertible preferred stock and convertible promissory notes in private placements, payments received under the Kaken Collaboration Agreement and, most recently, the public offering of common stock which closed on January 9, 2026. 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. The Company believes that, based on its current operating plan, its existing cash, cash equivalents and marketable securities of $ 308.5 million as of December 31, 2025, as well as net proceeds of $ 324.4 million, after deducting underwriting discounts and commissions from the public offering of common stock, which closed on January 9, 2026, will be sufficient to meet its operating and capital requirements for at least 12 months from the date of issuance of these consolidated financial statements. The Company will need to raise significant additional capital to fund ongoing research and development activities and maintain future operations. The Company’s management continuously monitors and, where necessary, may reduce its operating expenses in response to its clinical development progress and its ability and need to raise additional capital 125 Table of Contents ALUMIS INC. NOTES TO CONSOLIDATED FINANCIAL STATEMENTS through a combination of public and private equity, debt financings, strategic alliances and licensing arrangements. For example, should any of the Company’s ongoing trials not meet its clinical development objectives, the Company may scale back or discontinue related activities and reallocate its working capital to extend its ability to meet its operating and capital requirements. 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 planned 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 Basis of Presentation The accompanying consolidated financial statements and accompanying notes have been prepared in accordance with U.S. GAAP. The Company’s consolidated financial statements include the accounts of its subsidiaries, and all intercompany transactions were eliminated. The Company’s consolidated financial statements as of and for the year ended December 31, 2025, include the accounts of its subsidiaries ACELYRIN and WH2, LLC after the closing of the ACELYRIN Merger, and the accounts of Merger Sub from its incorporation in January 2025 until the ACELYRIN Merger. WH2, LLC has not had any operations or any balances since the closing of the ACELYRIN Merger. The Company’s consolidated financial statements as of and for the year ended December 31, 2024, included the accounts of FronThera U.S. Holdings, Inc. and FronThera U.S. Pharmaceuticals LLC, two wholly owned subsidiaries, prior to their dissolution. Any reference in these notes to applicable guidance is meant to refer to the authoritative U.S. GAAP as found in the 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 research and development expenses, valuation of acquired IPR&D intangible assets, revenue recognition, and stock-based compensation expense. 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 researching and developing medicines for autoimmune disorders. The chief executive officer, who is the chief operating decision maker (“CODM”), reviews financial information on an aggregate basis for purposes of allocating resources and evaluating financial performance (see Note 16 for additional information). 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 and cash equivalents, investments in marketable securities, accounts receivable and restricted cash. The Company maintains bank deposits in federally insured financial institutions and certain of 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 the financial institutions at which its bank deposits are maintained. 126 Table of Contents ALUMIS INC. NOTES TO CONSOLIDATED FINANCIAL STATEMENTS The Company also invests in money market funds, U.S. Treasury obligations, commercial paper, corporate debt obligations, supranational debt obligations, government development bank obligations and Federal agency obligations, which can be subject to certain credit risks. The Company mitigates the risks by 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. The Company considers a customer to be significant when revenues from that customer represent 10% or more of total revenues. All of the Company’s revenues are currently earned under its license and collaboration agreement with Kaken. As a result, the Company is subject to customer concentration risk. To date, the Company has not incurred any credit losses in connection with the Kaken Collaboration Agreement. 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 results of operations may be affected by worldwide economic conditions, which may continue to be impacted by global macroeconomic challenges and uncertainty in the markets, including international trade policies and tariffs, severely diminished liquidity and credit availability, rising inflation and monetary supply shifts, rising interest rates, labor shortages, declines in consumer confidence, declines in economic growth, increases in unemployment rates, recession risks and uncertainty about economic and geopolitical stability (for example, related to the evolving U.S. and ex-U.S. tariff landscape). These worldwide economic conditions have continued throughout 2025 and may negatively impact the Company’s business, financial position and results of operations. Business Acquisitions, Including Intangible Assets, Goodwill and Contingent Consideration The Company accounts for business combinations, as defined in ASC Topic 805, Business Combinations , using the acquisition method of accounting, which generally requires that assets acquired, including IPR&D intangible assets, and liabilities assumed, be recorded at fair value on the consolidated balance sheet as of the acquisition date. The excess of the fair value of the purchase consideration over the fair value of net assets acquired, if any, is recorded as goodwill on the consolidated balance sheet. The excess of the fair value of net assets acquired over the fair value of the purchase consideration, if any, represents negative goodwill, or a gain on bargain purchase, which is recognized in the consolidated statement of operations as of the date of the acquisition. Calculating the fair value of assets acquired and liabilities assumed requires the Company to make significant estimates and assumptions. As a result, the Company may record adjustments to the fair values within the measurement period, which may be up to one year from the acquisition date, with the corresponding offset to goodwill or a gain on bargain purchase. Transaction costs associated with business combinations are expensed as they are incurred. Intangible assets related to IPR&D projects acquired are considered to be indefinite-lived until abandonment or completion of the associated R&D efforts, which generally occurs when regulatory approval is obtained. Goodwill and indefinite-lived intangible assets are not amortized and, instead, are tested for impairment annually, in the fourth quarter, or more frequently if events or changes in circumstances indicate that it is more likely than not that the assets are impaired as 127 Table of Contents ALUMIS INC. NOTES TO CONSOLIDATED FINANCIAL STATEMENTS required by ASC 350 Intangibles - Goodwill and Other . Such events and circumstances may include a significant change in the Company’s business climate, economic and industry trends, legal factors, negative operating performance indicators, significant competition or changes in strategy. The Company performs testing of indefinite-lived intangible assets, other than goodwill, at the asset group level using a discounted cash flow model. If the carrying value exceeds the fair value, an impairment loss is recorded for that excess. The Company would also be required to reduce the carrying amounts of the related assets on its consolidated balance sheet. Determining the fair value of an indefinite-lived intangible asset group requires the application of judgment and involves the use of significant estimates and assumptions, including projections of future cash flows, which include estimated revenues, costs and probabilities of achieving technical and regulatory milestones, and discount rates, among other factors. The Company bases its fair value estimates on assumptions it believes to be reasonable, but which are unpredictable and inherently uncertain. Actual future results may differ from the estimates. Development costs incurred after an acquisition are expensed as they are incurred. Intangible assets with finite useful lives, which include completed IPR&D projects, are amortized over their estimated useful lives, primarily on a straight-line basis, and are also periodically reviewed for changes in facts or circumstances that may result in an impairment or in a reduction to the estimated useful life of the asset. In determining the initial fair value of an intangible asset, or when quantitative analysis is required to determine any impairment, the Company usually uses an income approach that discounts expected future cash flows to present value using a discount rate that is based on the estimated weighted-average cost of capital for comparable companies and represents the rate that market participants would use to value the intangible asset. These cash flow models require the use of Level 3 fair value measurements and inputs, including estimated revenues, costs and probabilities of technical and regulatory milestones, among other factors. If the Company is required to pay future consideration that is contingent upon the achievement of specified development, regulatory approval or sales-based milestone events, then the estimated fair value of contingent consideration liabilities is recognized in the consolidated balance sheet as of the date of the acquisition. Each reporting period thereafter, the Company revalues these obligations and records increases or decreases in their fair value on the consolidated statements of operations until such time that the payment is made or obligations expire. See Note 3 for additional information. Collaboration Arrangements and Revenue Recognition The Company earns revenue from collaboration agreements that allow collaborators to develop, manufacture and commercialize product candidates. Arrangements with collaborators may include intellectual property licenses, research and development services, manufacturing services for clinical and commercial supply and participation in joint steering committees. At the inception of an agreement, the Company evaluates if an agreement is a collaborative arrangement within the scope of ASC 808, Collaborative Arrangements (“ASC 808”). For collaborative arrangements that fall within the scope of ASC 808, the Company first determines which elements of the collaboration are deemed to be a performance obligation with a customer within the scope of ASC 606. For elements of collaboration arrangements that are accounted for pursuant to ASC 808 and are not subject to the guidance in ASC 606, the Company applies the revenue recognition model under ASC 606 or other guidance, as deemed appropriate. Under ASC 606, the Company recognizes revenue in an amount that reflects the consideration that the Company expects to receive in exchange for those goods or services when its collaborator, or customer, obtains control of promised goods or services. The Company follows a five-step approach: (i) identify the contract with a customer, (ii) identify the performance obligations in the contract, (iii) determine the transaction price, (iv) allocate the transaction price to the performance obligations and (v) recognize revenue when (or as) the customer obtains control of the product or service. The Company assesses the goods or services promised within the contract to determine whether each promised good or service is a performance obligation. Performance obligations are promises in a contract to transfer a distinct good or service to the customer that (i) the customer can benefit from on its own or together with other readily available resources and (ii) are separately identifiable from other promises in the contract. Goods or services that are not individually distinct performance obligations are combined with other promised goods or services until such combined group of promises meet 128 Table of Contents ALUMIS INC. NOTES TO CONSOLIDATED FINANCIAL STATEMENTS the requirements of a performance obligation. The Company determines the transaction price based on the amount of consideration the Company is entitled to receive in exchange for the transfer of control of a product or a service to the customer. Consideration may be fixed, variable, or a combination of both. Payments to the Company under these arrangements typically include one or more of the following: non-refundable upfront payments, reimbursement for research services, payments for clinical supplies, research, development or regulatory milestone payments, profit-sharing arrangements, and royalty and commercial sales milestone payments. Variable consideration, such as performance-based milestones, are included in the total consideration if the Company expects to receive such consideration and if it is probable that the inclusion of the variable consideration will not result in a significant reversal in the cumulative amount of revenue recognized under the arrangement. The Company accounts for cost reimbursements included in the transaction price using the expected value method. The Company excludes sales-based royalty and milestone payments from the total consideration it expects to receive until the underlying sales occur because the license to its intellectual property is deemed to be the predominant item to which the royalties or milestones relate as it is the primary driver of value in the collaboration arrangements. The Company then allocates the transaction price to each distinct performance obligation based on the relative standalone selling price. Key assumptions to determine the standalone selling price may include forecasted revenues, development timelines, probabilities of technical and regulatory success, and the expected level of effort for research and development services. The Company recognizes revenue associated with each performance obligation as the control over the promised goods or services transfer to its collaborators which occurs either at a point in time or over time. If control transfers over time, revenue is recognized by using a method of measuring progress that best depicts the transfer of goods or services. The Company evaluates the measure of progress and related inputs each reporting period and any resulting adjustments to revenue are recorded on a cumulative catch-up basis. Consideration allocated to options that include material rights is deferred until the options are exercised or expire. The Company records amounts as accounts receivable when the right to consideration is deemed unconditional. Consideration received that does not meet the requirements to satisfy ASC 606 revenue recognition criteria is recorded as deferred revenue in the consolidated balance sheets, classified as either current (less than 12 months) or non-current (more than 12 months) deferred revenue based on the Company’s best estimate of when such revenue will be recognized. See Note 7 for additional information. Cash and Cash Equivalents The Company considers all highly liquid investments purchased with an original maturity of three months or less to be cash equivalents. Restricted Cash Restricted cash represents security deposits in the form of letters of credit issued in connection with the Company’s leases (see Note 6 for additional information). Marketable Securities Marketable securities may consist of money market funds, U.S. Treasury obligations, commercial paper, corporate debt obligations, supranational debt obligations, government development bank obligations and Federal agency obligations with original maturities of more than three months at the time of purchase. As the Company’s entire investment portfolio is considered available for use in current operations, the Company classifies all marketable securities as available-for-sale and as current assets, even though the stated maturity may be more than one year from the current balance sheet date. Marketable securities are carried at fair value, with the change in fair value reported as unrealized gains or losses in accumulated other comprehensive income (loss), which is a separate component of stockholders’ equity (deficit) in the consolidated balance sheets. 129 Table of Contents ALUMIS INC. NOTES TO CONSOLIDATED FINANCIAL STATEMENTS The amortized cost of marketable securities is adjusted for amortization of premiums and accretion of discounts to maturity, which is included in interest income in the consolidated statements of operations and comprehensive loss. Realized gains and losses on the sale of securities are determined by specific identification of each security’s cost basis. The Company regularly reviews its investment portfolio to determine if any security is impaired, which would require it to record an allowance for credit losses or an impairment charge in the period any such determination is made. In making this judgment, the Company evaluates, among other things, the extent to which the fair value of a security is less than its amortized cost, its intent to sell or whether it is more likely than not that the Company will be required to sell the security before recovery of its amortized cost basis, the financial condition of the issuer and any changes thereto, and, as necessary, the portion of a decline in fair value that is credit-related. This assessment could change in the future due to new developments or changes in assumptions related to any particular security. Realized gains and losses, allowances for credit losses and impairments on available-for-sale marketable securities, if any, are recorded in the consolidated statements of operations and comprehensive loss. Fair Value Measurement Fair value is defined as the price that would be received to sell an asset or paid to transfer a liability in an orderly transaction between market participants at the measurement date. The carrying amounts of prepaid expenses, other current assets, accounts payable, accrued expenses and other liabilities approximate fair value due to their short-term maturities. Financial instruments, such as money market funds, marketable securities and derivative liabilities are measured at fair value at each reporting date (see Note 4 for additional information). Recoverable Value-Added Tax The Company conducts clinical trials in several European and Asian countries that can result in value-added tax (“VAT”) assessments based on the transfer of products across borders including production, packaging and distribution of clinical materials. VAT is a national tax that is levied at each stage of production and can vary by jurisdiction. When a company is not VAT-registered in a country, VAT is due when goods enter a country and is not considered reclaimable. When the Company becomes VAT-registered and establishes a pattern of VAT recoverability from taxing authorities in a certain country, the Company will record aggregate balances recoverable in other prepaid expenses and current assets in the consolidated balance sheets. The Company reviews these balances on a regular basis and records valuation allowances on the amounts that are not expected to be recovered. Deferred Offering Costs Deferred offering costs, consisting of legal, accounting and other third-party fees directly relating to in-process equity financings or offerings are capitalized. Deferred offering costs are 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 offering costs are expensed immediately as a charge to general and administrative expenses in the consolidated statements of operations and comprehensive loss. As of December 31, 2025 and 2024, the Company had $ 0.4 million and zero deferred offering costs, respectively, in other assets, non-current in its consolidated balance sheets. Property and Equipment, Net Property and equipment are stated at cost less accumulated depreciation and amortization. Depreciation is calculated using the straight-line method over the estimated useful lives of assets. Costs for capital assets not yet placed into service are capitalized as construction-in-progress and depreciated once placed into service. Repair and maintenance costs that are not considered improvements and do not extend the useful life of property and equipment, are expensed as incurred. Improvements are capitalized as additions to property and equipment. Upon sale or retirement of assets, the costs and related accumulated depreciation are removed from the consolidated balance sheets and the resulting gain or loss is reflected within operating expenses in the consolidated statements of operations and comprehensive loss. Asset Acquisitions and Acquired IPR&D Assets The Company measures and recognizes asset acquisitions that are not deemed to be business combinations based on the 130 Table of Contents ALUMIS INC. NOTES TO CONSOLIDATED FINANCIAL STATEMENTS cost to acquire the asset or group of assets, which includes transaction costs. The Company determines if the acquisition should be accounted for as an asset acquisition after considering whether substantially all of the fair value of the gross assets acquired is concentrated in a single asset or group of assets and whether the Company acquired a substantive process capable of significantly contributing to the Company’s ability to create outputs. Goodwill is not recognized in asset acquisitions. If acquired in-process technology assets, including licenses, know-how and patents are determined to not have an alternative future use, the cost is charged to research and development expenses at the acquisition date. The Company accounts for contingent consideration identified in an asset acquisition that does not meet the definition of a derivative under ASC 815, Derivatives and Hedging , when the payment becomes probable and reasonably estimable. Such amounts are expensed or capitalized based on the nature of the associated asset at the date the related contingency is recognized. ​ Leases The Company determines whether an arrangement is or contains a lease at the inception of the arrangement and whether such a lease should be classified as a financing lease or operating lease at the commencement date of the lease. Leases with a term greater than one year are classified as operating lease right-of-use assets, net and operating lease liabilities, current and non-current in the consolidated balance sheets. The Company elected not to recognize the right-of-use assets and lease liabilities for leases with lease terms of one year or less (short-term leases). Lease liabilities and their corresponding right-of-use assets are recorded based on the present value of lease payments over the lease term. The Company considers the lease term to be the noncancelable period that it has the right to use the underlying asset, together with any periods where it is reasonably certain it will exercise an option to extend (or not terminate) the lease. As the interest rate implicit in the Company’s lease contracts is not readily determinable, the Company utilizes its incremental borrowing rate to determine the present value of lease payments. The incremental borrowing rate is derived from information available at the lease commencement date and represents the rate of interest that a lessee would have to pay to borrow an amount equal to the lease payments on a collateralized basis over a similar term in a similar economic environment. Rent expense for operating leases is recognized on a straight-line basis over the lease term. The Company has elected to not separate lease and non-lease components for its real estate leases and instead accounts for each separate lease component and the non-lease components associated with that lease component as a single lease component. Variable lease payments are recognized as incurred. As of December 31, 2025 and 2024, the Company had no finance leases. Impairment of Definite-Lived Long-Lived Assets The Company regularly reviews the carrying value and estimated lives of all of its definite-lived long-lived assets, including property and equipment, and right-of-use assets to determine whether indicators of impairment may exist that warrant adjustments to carrying values or estimated useful lives. Recoverability of assets to be held and used is measured by a comparison of the carrying amount of an asset group to future undiscounted net cash flows expected to be generated by the asset or asset group. Should impairment exist, the impairment loss to be recognized is measured by the amount by which the carrying amount of the asset exceeds the projected discounted future net cash flows arising from the asset. Derivative Liability The Company may issue financial instruments, such as promissory notes, that include embedded derivatives, such as call options. Derivatives are accounted for under ASC 815, Derivatives and Hedging . The Company performs analysis of derivatives embedded in the financial instruments, and if any require bifurcation, accounts for these at fair value at the issuance date. A derivative liability is accounted for separately from the financial instrument at fair value on the issuance date and is remeasured each reporting period. The changes in the fair value of the derivative liability are included in change in fair value of derivative liability in the consolidated statements of operations and comprehensive loss. 131 Table of Contents ALUMIS INC. NOTES TO CONSOLIDATED FINANCIAL STATEMENTS In March 2024, in connection with the Company’s redeemable convertible preferred stock financings, the Company issued options to purchase additional shares of redeemable convertible preferred stock at a specified price, which were accounted for as derivative liabilities. Changes in fair value of these derivative liabilities were included in the other income (loss) in the consolidated statement of operations and comprehensive loss for each reporting period until the derivatives were settled in May 2024 (see Note 4). Redeemable Convertible Preferred Stock The Company recorded redeemable convertible preferred stock at their respective fair values on the dates of issuance, net of offering costs. The redeemable convertible preferred stock was recorded outside of permanent equity because while it was not mandatory, redemption was contingent upon the occurrence of certain events considered not solely within the Company’s control. The Company did not adjust the carrying values of the redeemable convertible preferred stock to the liquidation preferences of such stock, because it was uncertain whether or when a deemed liquidation event would occur that would obligate the Company to pay the liquidation preferences to holders of redeemable convertible preferred stock. Subsequent adjustments to the carrying values to the liquidation preferences would be made only when it became probable that such a deemed liquidation event would occur. All redeemable convertible preferred stock outstanding was converted into common stock immediately prior to the closing of the IPO on July 1, 2024, and the Company had no outstanding redeemable convertible preferred stock outstanding as of December 31, 2025 and 2024. Research and Development Expenses and Accruals Research and development costs are expensed as incurred. Research and development costs consist primarily of costs associated with acquiring technology and intellectual property licenses that have no alternative future uses, costs incurred under in-license or assignment agreements, salaries and benefits of research and development personnel, costs related to research activities, preclinical studies, clinical trials, drug manufacturing, third-party professional research and development consulting services, and allocated overhead and facility-related expenses. Payments associated with licensing agreements to acquire exclusive licenses to develop, use, manufacture and commercialize products that have not reached technological feasibility and do not have alternate future use will also be expensed as incurred. The Company records accrued liabilities for estimated costs of its research and development activities conducted by third-party service providers. The Company accrues these costs based on factors such as estimates of the work completed and in accordance with the third-party service agreements. If the Company does not identify costs that have begun to be incurred or if the Company underestimates or overestimates the level of services performed or the costs of these services, actual expenses could differ from the estimates. To date, the Company has not experienced any material differences between accrued costs and actual costs incurred. Nonrefundable advance payments for goods or services to be received in the future for use in research and development activities are recorded as prepaid expenses. The prepaid amounts are expensed as the related goods are delivered or the services are performed and classified as current or non-current prepaid expenses and other assets. The Company makes payments in connection with clinical trials to CMOs that manufacture the materials for its product candidates and to CROs and clinical trial sites that conduct and manage the Company’s clinical trials. The financial terms of these contracts are subject to negotiation, which vary by contract and may result in payments that do not match the periods over which materials or services are provided. Generally, these agreements set forth the scope of work to be performed at a fixed fee, unit price or on a time and materials basis. The Company makes estimates of accrued research and development expenses as of each balance sheet date based on facts and circumstances known at that time. The Company periodically confirms the accuracy of its estimates with the service providers and makes adjustments, if necessary. Research and development accruals are estimated based on the level of services performed, progress of the studies, including the phase or completion of events, and contracted costs. The estimated costs of research and development services provided, but not yet invoiced, are included in accrued expenses in the consolidated balance sheets. If the actual timing of the performance of services or the level of effort varies from the original estimates, the Company will adjust the accrual accordingly. 132 Table of Contents ALUMIS INC. NOTES TO CONSOLIDATED FINANCIAL STATEMENTS Comprehensive Loss Comprehensive loss represents all changes in stockholders’ deficit except those resulting from distributions to stockholders. The Company’s other comprehensive income (loss) for the years ended December 31, 2025 and 2024 consisted of unrealized gain (loss) on marketable securities, net of taxes. Patent Costs All patent-related costs incurred in connection with filing and prosecuting patent applications are expensed as incurred due to the uncertainty about the recovery of the expenditure. Amounts incurred are classified as general and administrative expenses in the consolidated statements of operations and comprehensive loss. Stock-Based Compensation Expense The Company accounts for stock-based compensation expense in accordance with ASC 718. The Company grants stock-based awards to employees, directors and non-employee consultants in the form of stock options and RSUs to purchase shares of its common stock. The Company measures stock options granted with service-based vesting based on the fair value of the award on the grant date using the Black-Scholes option-pricing model. The model requires management to make a number of assumptions, including common stock fair value, expected volatility, expected term, risk-free interest rate and expected dividend yield. The Company expenses the fair value of its stock-based compensation awards on a straight-line basis over the requisite service period, which is the period in which the related services are received. The Company has also granted stock options with graded vesting based on market, service and performance conditions. At the grant date, the fair value of these stock options was estimated using a Monte Carlo simulation model, which uses a distribution of potential outcomes over the vesting period. The assumptions utilized in the calculation included the Company’s expected common stock price, expected volatility, risk-free rate and expected term. Stock-based compensation expense for these awards is recognized on a straight-line basis over the requisite service period, which is the longer of the explicit service period of the service condition and the derived service period of the market condition, as determined for each separately vesting portion of the awards as if each award was, in substance, multiple awards. Stock-based compensation expense related to stock purchase rights under the Company’s 2024 ESPP is measured based on grant date at fair value using the Black-Scholes option-pricing model. The model requires management to make a number of assumptions, including common stock fair value, expected volatility, expected term, risk-free interest rate and expected dividend yield. Stock-based compensation expense is recognized on a straight-line basis over the offering period The Company accounts for award forfeitures as they occur and classifies stock-based compensation expense in its consolidated statements of operations and comprehensive loss in the same manner in which the award recipient’s salary or services costs are classified. Income Taxes The Company accounts for income taxes using the asset and liability method, which requires the recognition of deferred tax assets and liabilities for the expected future tax consequences of events that have been recognized in the consolidated financial statements or in the Company’s tax returns. Deferred tax assets and liabilities are determined based on the difference between the financial statement and tax basis of assets and liabilities using enacted tax rates in effect for the year in which the differences are expected to reverse. Changes in deferred tax assets and liabilities are recorded in the provision for income taxes. The Company assesses the likelihood of deferred tax assets being realized. It provides a valuation allowance when it is more likely than not that some portion or all of a deferred tax asset will not be realized. The ultimate realization of deferred tax assets is dependent upon the generation of future taxable income during the periods in which the temporary differences representing net future deductible amounts become deductible. 133 Table of Contents ALUMIS INC. NOTES TO CONSOLIDATED FINANCIAL STATEMENTS The Company recognizes the tax benefit from an uncertain tax position if it is more likely than not that the tax position will be sustained upon examination by the tax authorities, based on the merits of the position. The Company’s policy is to recognize interest and penalties related to the underpayment of income taxes as a component of income tax expense or benefit. To date, there have been no interest or penalties incurred in relation to unrecognized tax benefits. Net Loss Per Share Attributable to Common Stockholders Basic and diluted net loss per share attributable to common stockholders is presented in conformity with the two-class method required for participating securities. As such, net income is attributed to common stockholders and participating securities based on their participation rights. Prior to the IPO, under the two-class method, the net loss attributable to common stockholders was not allocated to the redeemable convertible preferred stock as the holders of the redeemable convertible preferred stock did not have a contractual obligation to share in the Company’s losses. Upon the IPO, the Company’s redeemable convertible preferred stock converted into either Class A or Class B common stock, and were immediately thereafter redesignated into voting and non-voting common stock, respectively, and therefore are included in the allocation of net loss attributable to common stockholders as they share in the Company’s losses. Voting and non-voting common stock participate in the Company’s losses equally. Basic net loss per share attributable to common stockholders is computed by dividing the net loss attributable to common stockholders by the weighted-average number of shares of common stock outstanding during the period. Diluted net loss per share is computed by dividing the net loss attributable to common stockholders by the weighted-average number of shares of common stock and potentially dilutive securities outstanding for the period. Potentially dilutive securities include stock options and RSUs issued and outstanding, early exercised stock options, and unvested restricted common stock. As the Company has reported losses for all periods presented, all potentially dilutive securities are antidilutive and accordingly, basic net loss per share equals diluted net loss per share. 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 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 private companies, the Company will adopt the new or revised standard at the time private 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 private companies. Recently Adopted Accounting Pronouncements In December 2023, the FASB issued ASU No. 2023-09, Income Taxes (Topic 740): Improvements to Income Tax Disclosures (“ASU 2023-09”), which requires the disclosure of specific categories in the rate reconciliation and greater disaggregation for income taxes paid. ASU 2023-09 is effective for annual periods beginning after December 15, 2024 for public entities and for fiscal years beginning after December 15, 2025 for all other entities, with early application permitted. ASU 2023-09 should be adopted prospectively with the option to be adopted retrospectively. The Company adopted this standard prospectively effective for the year ended December 31, 2025 and reflected the required annual income tax disclosures in the notes to its consolidated financial statements (see Note 15). Recently Issued and Not Yet Adopted Accounting Pronouncements In November 2024, the FASB issued ASU No. 2024-03, Disaggregation of Income Statement Expenses (Topic 220) (“ASU 2024-03”), requiring that public business entities disclose additional information about specific expense categories in the notes to financial statements at interim and annual reporting periods. The amendments of ASU 2024-03 are effective for annual reporting periods beginning after December 15, 2026, and interim reporting periods beginning after December 15, 2027. The requirements of ASU 2024-03 may be applied either prospectively to financial statements issued for reporting periods after the effective date or retrospectively to any or all prior periods presented in the financial statements. The 134 Table of Contents ALUMIS INC. NOTES TO CONSOLIDATED FINANCIAL STATEMENTS Company is currently evaluating the impact of adopting ASU 2024-03 on its consolidated financial statements and disclosures. In December 2025, the FASB issued ASU No. 2025-11, Interim Reporting (Topic 270): Narrow-Scope Improvements (“ASU 2025-11”), which clarifies the form and content of interim financial statements, adds a comprehensive list of required interim disclosures, and provides a disclosure principle for condensed interim financial statements. ASU 2025-11 is effective for interim reporting periods within annual reporting periods beginning after December 15, 2027. Early adoption is permitted and, on adoption, can be applied either prospectively or retrospectively to any or all periods presented in the financial statements. The Company is currently evaluating the impact of the new standard on the Company's consolidated financial statements and related disclosures. 3. Acquisition ACELYRIN Merger The Company completed its acquisition of ACELYRIN on the Closing Date of May 21, 2025 and accounted for the transaction as an acquisition under ASC Topic 805, Business Combinations . ACELYRIN was a late-stage biopharma company focused on identifying, acquiring, and accelerating the development and commercialization of transformative medicines. ACELYRIN’s portfolio consisted of lonigutamab, a subcutaneously delivered, monoclonal antibody targeting IGF-1R for the potential treatment of Thyroid Eye Disease (“TED”). The ACELYRIN Merger strengthened the Company’s balance sheet and its cash position and added the lonigutamab product candidate to the Company’s development portfolio as of the Closing Date. As of the Closing Date, the Company (i) issued 48,653,549 shares of its common stock in exchange for ACELYRIN’s issued and outstanding common stock shares and paid cash for fractional shares, (ii) assumed ACELYRIN’s stock options with an exercise price of $ 18.00 or less outstanding and unexercised immediately prior to the Closing Date, which are exercisable into 4,712,186 shares of the Company’s common stock, (iii) assumed ACELYRIN’s RSUs outstanding and unvested immediately prior to the Closing Date, which were converted into 1,323,905 of the Company’s RSUs, and (iv) assumed ACELYRIN’s performance RSUs outstanding and unvested immediately prior to the Closing Date, which were converted into 146,963 of the Company’s RSUs subject only to a service vesting condition. Outstanding shares, stock options, RSUs and performance RSUs were exchanged at the exchange ratio of 0.4814 shares of the Company’s common stock for each share of ACELYRIN common stock (the “Exchange Ratio”). ACELYRIN’s outstanding and unexercised options with exercise prices more than $ 18.00 were cancelled. Exercise prices for the assumed options were determined as the product of the original exercise prices multiplied by the reciprocal of the Exchange Ratio. Converted ACELYRIN stock options and RSUs continue to vest in accordance with their original terms. Performance RSUs were deemed to have 100 % satisfied their performance conditions and will vest in two equal installments on May 15 of calendar years 2026 and 2027, subject to the holder of the converted performance RSUs remaining in service with the Company or any of its subsidiaries on such date. The purchase price consideration consists of the Company’s shares of common stock issued as of the Closing Date and the additional stock-based compensation related to the fair value of replacement awards attributable to pre-combination services, and is calculated as follows (in thousands, except share and per share amounts): ​ ​ ​ ​ Implied shares of common stock issued to holders of ACELYRIN common stock ​ ​ 48,653,549 Closing price per share of common stock as of Closing Date ​ $ 4.78 Consideration transferred for share exchange ​ $ 232,564 Fair value of replacement awards attributable to pre-combination services ​ $ 5,513 Total purchase price consideration ​ $ 238,077 ​ The ACELYRIN Merger was accounted for as a business combination with the Company being treated as the accounting 135 Table of Contents ALUMIS INC. NOTES TO CONSOLIDATED FINANCIAL STATEMENTS acquirer. Net assets acquired were recognized at their fair value as of the Closing Date of the ACELYRIN Merger. The Company recognized ACELYRIN Merger transaction costs of $ 14.7 million in general and administrative expenses in the consolidated statements of operations and comprehensive loss for the year ended December 31, 2025. The following table presents the final purchase price allocation of the fair value of the net assets acquired and liabilities assumed as of the Closing Date (in thousands): ​ ​ ​ ​ ​ Assets Acquired ​ ​ Cash and cash equivalents ​ $ 49,155 Restricted cash ​ 367 Marketable securities ​ 333,436 Research and development prepaid expenses ​ 958 Prepaid credit voucher for clinical manufacturing ​ ​ 11,376 Other prepaid expenses and current assets ​ 8,081 Restricted cash, non-current ​ 220 Property and equipment ​ 420 Intangible assets ​ ​ 50,959 Operating lease right-of-use assets ​ 4,349 Other assets, non-current ​ 744 Total assets ​ $ 460,065 Liabilities Assumed ​ ​ Accounts payable ​ $ ( 6,518 ) Research and development accrued expenses ​ ( 3,546 ) Other accrued expenses and current liabilities ​ ( 5,688 ) Operating lease liabilities, current ​ ( 1,390 ) Operating lease liabilities, non-current ​ ( 6,238 ) Deferred tax liability ​ ( 10,701 ) Total liabilities ​ ( 34,081 ) Fair value of net assets ​ $ 425,984 Purchase consideration ​ ​ 238,077 Gain on bargain purchase ​ $ 187,907 ​ The acquisition method requires, among other things, that assets acquired and liabilities assumed in a business combination be recognized at their fair values as of the Closing Date. Valuing certain components of the ACELYRIN Merger, primarily the acquired IPR&D intangible asset and a deferred tax liability required the Company to make significant estimates and assumptions. The valuation of assets acquired and liabilities assumed was finalized during the three months ended December 31, 2025, which did not result in any measurement period adjustments. Intangible assets represent the acquired IPR&D intangible asset related to the acquired lonigutamab product candidate in development as of the Closing Date. The fair value of the acquired IPR&D intangible asset was calculated as $ 51.0 million using the multi-period excess earnings method, which is equal to the present value of the incremental after-tax cash flows attributable to that intangible asset, using a discount rate of 24.0 % based on the best estimate of a market participant's after-tax weighted average cost of capital. Projected future cash flows were based on significant estimates, including estimated revenues, costs and probabilities of achieving technical and regulatory milestones, among other factors. The acquired IPR&D intangible asset is an indefinite-lived intangible asset and is subject to an annual impairment test. The Company performed a quantitative analysis for its annual impairment assessment of the acquired IPR&D intangible asset as of December 31, 2025. The quantitative analysis utilized a discounted cash flow model with assumptions that are considered level 3 inputs and concluded that the acquired IPR&D intangible asset had a fair value in excess of its carrying value as of December 31, 2025, and therefore no impairment was identified. The Company acquired a prepaid credit voucher for clinical manufacturing issued by one of ACELYRIN’s contract 136 Table of Contents ALUMIS INC. NOTES TO CONSOLIDATED FINANCIAL STATEMENTS manufacturers that will be applied towards payments of clinical product manufacturing invoices issued by the vendor. The remaining balance of $ 11.4 million as of the Closing Date was not adjusted from its carrying amount as its fair value approximated its carrying value as of this date. The Company acquired two operating leases and a sublease. Refer to Note 9 for additional details. The Company estimated the fair value of lease liabilities as the present value of the remaining lease payments, as if the acquired leases were new leases of the acquirer as of the Closing Date. The Company measured the right-of-use asset at the same amount as the lease liability as adjusted to reflect favorable or unfavorable terms of the lease when compared with market terms. As ACELYRIN entered into a sublease in February 2025, these sublease terms were considered at market terms. As of the Closing Date, the fair value of operating lease liabilities, current, increased by $ 0.2 million and the fair value of operating lease liabilities, non-current, increased by $ 0.5 million. As of the Closing Date, the fair value of operating lease right-of-use assets, net, decreased by $ 0.1 million. Because the fair value of the identifiable assets acquired and liabilities assumed exceeded the fair value of the purchase consideration transferred, the Company recorded a gain on bargain purchase of $ 187.9 million as of the Closing Date. Consequently, the Company reassessed the recognition and measurement of identifiable assets acquired and liabilities assumed in accordance with ASC 805-30-25-4 and concluded that all acquired assets and assumed liabilities were recognized and that the valuation procedures and resulting measures were appropriate. Gain on bargain purchase primarily relates to the market value of ACELYRIN’s common stock trading below the carrying value of net assets and the Exchange Ratio being fixed at the time the Merger Agreement was signed and not adjusted for subsequent changes in the market price of the Company’s common stock. Gain on bargain purchase is recognized as other income in the consolidated statements of operations and comprehensive loss. The Company recognized a deferred tax liability of $ 10.7 million related to the acquired IPR&D intangible asset as of the Closing Date. The Company also has additional severance related obligations under the Merger Agreement that are separate from the assets and liabilities acquired. In accordance with the ACELYRIN severance plan, ACELYRIN employees terminated without cause within 12 months of the Closing Date are entitled to receive severance benefits, including acceleration of their outstanding equity awards and extension of their outstanding options exercise periods of up to 12 months post-termination. The Company estimated total cash severance obligation, including related taxes, of $ 11.9 million, which it expects to pay within 12 months from the Closing Date based on agreed termination dates with employees. Severance obligation is recorded to expense over the remaining employment period for notified employees. The Company recognized $ 6.5 million as general and administrative expenses and $ 5.4 million as research and development expenses related to severance expenses for the year ended December 31, 2025. As of December 31, 2025, the severance liability of $ 0.2 million is classified as other accrued expenses and current liabilities in the consolidated balance sheet. The Company estimated stock-based compensation expense of $ 13.1 million related to the accelerated vesting and exercise term modification for severed employees, which was recognized in the year ended December 31, 2025. The Company recognized stock-based compensation expense of $ 9.0 million as general and administrative expenses and $ 4.1 million as research and development expenses for the year ended December 31, 2025. Following the Closing Date, the operating results of ACELYRIN have been included in the Company’s consolidated financial statements. For the period from May 22, 2025 through December 31, 2025, there was no revenue attributable to ACELYRIN, and operating losses attributable to ACELYRIN for such period were $ 9.3 million. ​ The ACELYRIN Merger is intended to be a reorganization under Internal Revenue Code Section 368(a). The Merger Agreement outlines the “plan of reorganization” within the meaning of the regulations issued under Internal Revenue Code Section 368(a) and the ACELYRIN Merger is intended to qualify as a tax-free reorganization for U.S. federal and state income tax purposes. 137 Table of Contents ALUMIS INC. NOTES TO CONSOLIDATED FINANCIAL STATEMENTS Unaudited Pro Forma Summary of Operations The following table shows the unaudited pro forma summary of operations for the years ended December 31, 2025 and 2024, as if the ACELYRIN Merger had closed on January 1, 2024. The pro forma financial information is provided for comparative purposes only and is not necessarily indicative of what actual results would have been had the acquisition occurred as of January 1, 2024, nor does it give effect to synergies or any cost savings, and it is not indicative of what such results would be for any future period: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year Ended December 31, ​ ​ 2025 ​ ​ ​ 2024 Total revenue ​ $ 24,050 ​ $ — Net loss ​ ​ ( 475,071 ) ​ ​ ( 394,155 ) ​ The summary pro forma financial information includes the following adjustments: ● actual ACELYRIN Merger transaction costs of $ 14.7 million were excluded from the year ended December 31, 2025 pro forma results, and included in the year ended December 31, 2024 pro forma results, as if these costs were incurred during the 2024 period; ● incremental stock-based compensation expense related to the accelerated vesting and exercise term modification of $ 13.1 million was excluded from the years ended December 31, 2025 pro forma results, and included in the year ended December 31, 2024 pro forma results, as if this expense was incurred during the 2024 period; ● severance cash obligation expense for terminated ACELYRIN employees of $ 11.9 million was excluded from the year ended December 31, 2025 pro forma results, and included in the year ended December 31, 2024 pro forma results, as if this expense was incurred during the 2024 period; and ● Gain on bargain purchase of $ 187.9 million was excluded from the year ended December 31, 2025 pro forma results, and included in the year ended December 31, 2024 pro forma results, as if such gain was recognized during the 2024 period. 4. 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. 138 Table of Contents ALUMIS INC. NOTES TO CONSOLIDATED FINANCIAL STATEMENTS 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. Treasury obligations. Level 2 financial instruments are comprised of U.S. Treasury obligations, corporate debt obligations, commercial paper, supranational debt obligations and government development bank obligations. 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 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 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 present the Company’s fair value hierarchy for financial assets measured at fair value on a recurring basis as of December 31, 2025 and 2024 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, 2025 ​ ​ ​ ​ Level 1 ​ ​ ​ Level 2 ​ ​ ​ Level 3 ​ ​ ​ Total Assets: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Cash equivalents ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Money market funds ​ $ 81,729 ​ $ — ​ $ — ​ $ 81,729 U.S. treasuries ​ 3,971 ​ ​ — ​ ​ — ​ 3,971 Marketable securities ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ U.S. Treasury obligations ​ ​ 110,809 ​ ​ 37,673 ​ ​ — ​ ​ 148,482 Corporate debt obligations ​ ​ — ​ ​ 30,743 ​ ​ — ​ ​ 30,743 Commercial paper ​ ​ — ​ ​ 27,672 ​ ​ — ​ ​ 27,672 Supranational debt obligations ​ ​ — ​ ​ 7,922 ​ ​ — ​ ​ 7,922 Government development bank obligations ​ — ​ 4,012 ​ — ​ 4,012 Total assets ​ $ 196,509 ​ $ 108,022 ​ $ — ​ $ 304,531 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, 2024 ​ ​ ​ ​ Level 1 ​ ​ ​ Level 2 ​ ​ ​ Level 3 ​ ​ ​ Total Assets: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Cash equivalents ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Money market funds ​ $ 168,847 ​ $ — ​ $ — ​ $ 168,847 Marketable securities ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ U.S. Treasury obligations ​ 47,137 ​ 71,600 ​ — ​ 118,737 Total assets ​ $ 215,984 ​ $ 71,600 ​ $ — ​ $ 287,584 ​ ​ 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. ​ ​ 139 Table of Contents ALUMIS INC. NOTES TO CONSOLIDATED FINANCIAL STATEMENTS The following table provides a range of assumptions used in the valuation of the derivative liability for the year ended December 31, 2024: ​ ​ ​ ​ ​ Year Ended December 31, ​ ​ ​ ​ 2024 Expected term (in years) ​ 0.2 – 0.4 Volatility ​ 55.1 % – 59.9 % Risk-free interest rate ​ 5.4 % – 5.5 % Dividend yield ​ 0.00 % Probability of option exercise ​ 0.0 % – 100.0 % ​ The following table provides a roll-forward of the fair value of the Company’s Level 3 financial instruments, the derivative liability, for the year ended December 31, 2024 (in thousands): ​ ​ ​ ​ Year Ended December 31, ​ 2024 Fair value at beginning of period $ — Fair value upon issuance ​ 8,913 Changes in fair value ​ 5,406 Fair value upon settlement ​ ( 14,319 ) Fair value at end of period $ — ​ The Company did not hold Level 3 financial instruments for the year ended December 31, 2025. There were no transfers between Level 1, Level 2 or Level 3 categories for the years ended December 31, 2025 and 2024. 5. Marketable Securities Marketable securities, which are classified as available-for-sale, consisted of the following as of December 31, 2025 and 2024 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, 2025 ​ ​ ​ ​ ​ Gross ​ Gross ​ ​ ​ ​ ​ Amortized Cost ​ Unrealized ​ Unrealized ​ Fair ​ ​ Basis ​ Gains ​ Losses ​ Value Short-term marketable securities: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ U.S. Treasury obligations ​ $ 148,352 ​ $ 129 ​ $ — ​ $ 148,481 Corporate debt obligations ​ ​ 30,720 ​ ​ 24 ​ ​ — ​ ​ 30,744 Commercial paper ​ ​ 27,652 ​ ​ 20 ​ ​ — ​ ​ 27,672 Supranational debt obligations ​ ​ 7,913 ​ ​ 9 ​ ​ — ​ ​ 7,922 Government development bank obligations ​ ​ 4,006 ​ ​ 6 ​ ​ — ​ ​ 4,012 Total short-term marketable securities ​ $ 218,643 ​ $ 188 ​ $ — ​ $ 218,831 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, 2024 ​ ​ ​ ​ Gross ​ Gross ​ ​ ​ ​ Amortized Cost ​ Unrealized ​ Unrealized ​ Fair ​ ​ Basis ​ Gains ​ Losses ​ Value Short-term marketable securities: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ U.S. Treasury obligations ​ $ 118,697 ​ $ 45 ​ $ ( 5 ) $ 118,737 Total short-term marketable securities ​ $ 118,697 ​ $ 45 ​ $ ( 5 ) $ 118,737 ​ ​ All marketable securities held as of December 31, 2025 and 2024 had contractual maturities of less than one year. 140 Table of Contents ALUMIS INC. NOTES TO CONSOLIDATED FINANCIAL STATEMENTS As of December 31, 2025 and 2024, 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 marketable securities were not significantly impacted. For all marketable 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 expected credit losses was recorded for the years ended December 31, 2025 and 2024. 6. Balance Sheet Components Restricted cash Restricted cash includes cash held at financial institutions that is pledged as collateral for stand-by letters of credit of $ 1.3 million and $ 1.1 million related to lease commitments as of December 31, 2025 and 2024, respectively. The cash will be restricted until the termination or modification of the related lease agreements. Restricted cash is classified as restricted cash, non-current in the consolidated balance sheets as of December 31, 2025 and 2024. Other Prepaid Expenses and Current Assets Other prepaid expenses and current assets consisted of the following as of December 31, 2025 and 2024 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, ​ ​ ​ December 31, ​ ​ 2025 ​ 2024 Prepaid subscriptions ​ $ 2,088 ​ $ 1,232 Interest receivable ​ ​ 1,343 ​ ​ 698 Prepaid insurance ​ ​ 744 ​ ​ 695 Tax receivable ​ ​ 740 ​ ​ 1,114 Prepaid credit voucher for clinical manufacturing ​ ​ 683 ​ ​ — Other ​ 1,142 ​ 762 Total other prepaid expenses and current assets ​ $ 6,740 ​ $ 4,501 ​ The prepaid credit voucher for clinical manufacturing was received by ACELYRIN in the third quarter of 2024 as part of an agreement to cancel certain services with a vendor under a manufacturing agreement related to the suspension of development of certain ACELYRIN programs. The prepaid credit voucher for clinical manufacturing may be used to settle invoices for services and raw materials from this vendor related to the lonigutamab product candidate. As of December 31, 2025, the prepaid credit voucher for clinical manufacturing included $ 0.7 million classified in other prepaid expenses and current assets and $ 5.5 million included in other assets, non-current. 141 Table of Contents ALUMIS INC. NOTES TO CONSOLIDATED FINANCIAL STATEMENTS Property and Equipment, net Property and equipment, net consisted of the following as of December 31, 2025 and 2024 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Estimated Useful Life ​ ​ ​ December 31, ​ ​ ​ December 31, ​ ​ (in years) ​ 2025 ​ 2024 Leasehold improvements Shorter of useful life or lease term ​ $ 17,655 ​ $ 17,618 Laboratory equipment 5 ​ ​ 5,843 ​ ​ 5,227 Furniture and fixtures 5 ​ 1,709 ​ 1,709 Computer equipment 5 ​ 896 ​ 896 Capitalized software 3 ​ 75 ​ 75 Total property and equipment, gross ​ ​ ​ 26,178 ​ 25,525 Less: Accumulated depreciation and amortization ​ ​ ​ ( 7,988 ) ​ ( 4,557 ) Total property and equipment, net ​ ​ ​ $ 18,190 ​ $ 20,968 ​ Depreciation and amortization expense was $ 3.5 million and $ 3.2 million for the years ended December 31, 2025 and 2024, respectively. Other Accrued Expenses and Current Liabilities Other accrued expenses and current liabilities consisted of the following as of December 31, 2025 and 2024 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, ​ ​ ​ December 31, ​ ​ 2025 ​ 2024 Accrued personnel and related expenses ​ $ 17,581 ​ $ 7,765 Accrued professional services and other ​ 4,397 ​ 2,657 Severance liability ​ ​ 244 ​ ​ — Accrued other expenses ​ 81 ​ 158 Total other accrued expenses and current liabilities ​ $ 22,303 ​ $ 10,580 ​ 7. Revenue Kaken Collaboration Agreement On March 25, 2025, (the “Effective Date”) the Company entered into the Kaken Collaboration Agreement. Under the terms of the Collaboration Agreement, the Company granted to Kaken an exclusive right to develop, manufacture and commercialize envu, formerly known as ESK-001, for dermatology indications in Japan, with options to expand the license, subject to opt-in payments and certain cost-sharing obligations on the part of Kaken, to include rheumatological and gastrointestinal diseases. Pursuant to the terms of the Collaboration Agreement, the Company is responsible for the global development of envu in the dermatology field, and Kaken is responsible for the clinical development, regulatory approvals and commercialization of envu in Japan in dermatology and other indications for which Kaken has exercised its option. Kaken is required to use commercially reasonable efforts to conduct all subsequent development, manufacture, and commercialization activities. The Collaboration Agreement further provides that the Company will retain rights to envu in all other indications and geographies. In March 2025, Kaken made an upfront, non-refundable payment of $ 20.0 million to the Company. In addition, Kaken will pay the Company an aggregate of $ 20.0 million towards global development costs for envu in the dermatology field through the end of 2026 and thereafter will pay a specified share of development costs applicable to the dermatology field, and for any field for which Kaken exercises its option, subject to Kaken's right to opt out of cost-sharing in certain 142 Table of Contents ALUMIS INC. NOTES TO CONSOLIDATED FINANCIAL STATEMENTS indications in specified circumstances. In addition, Kaken would pay the Company up to an aggregate of $ 36.0 million upon the achievement of regulatory milestones and upon Kaken’s exercise of its field expansion options for the rheumatology and gastrointestinal fields. In addition, the Company is entitled to receive aggregate payments of up to ¥ 15.5 billion upon the achievement of commercial milestones, plus tiered royalties at percentages ranging from the low double digits into the twenties on aggregate net sales of envu in Japan. The Company evaluated the Collaboration Agreement and concluded it was within the scope of ASC 606. As of the Effective Date, the Company identified four performance obligations: (1) license to develop, manufacture and commercialize envu (the “License Obligation”), (2) development services that support the global development of envu (the “Development Services Obligation”), (3) the manufacture of the clinical supply in Japan (the “Manufacturing Services Obligation”) and (4) a material right related to the option for rheumatology disease (the “Material Right Obligation”). The License Obligation was considered functional intellectual property and distinct from other promises under the contract, as Kaken can benefit from the license on its own or together with other readily available resources. The Development Services Obligation and Manufacturing Services Obligation were considered distinct as Kaken could benefit from both of these separately with the license transferred by the Company at the inception of the agreement. The option in the rheumatology field contained a material right because its exercise does not require payment of a fee that is commensurate with the value of the additional license. No material right was assigned to the gastrointestinal field since its estimated fair value did not exceed the exercise price of the option. The transaction price includes the upfront license fee of $ 20.0 million, the global development cost reimbursement of $ 20.0 million in the dermatology field through the end of 2026, the estimated global development cost reimbursement in the dermatology field after 2026 of $ 1.5 million and an immaterial amount of variable consideration related to the Manufacturing Services Obligation. The Company determined that any variable consideration related to development and regulatory milestones was deemed to be fully constrained at inception and therefore excluded from the initial transaction price due to the high degree of uncertainty and risk associated with these potential payments, and the Company could not assert that it was probable that a significant reversal in the amount of cumulative revenue recognized would not occur. The Company developed the estimated standalone selling prices for the License Obligation and Material Right Obligation primarily based on the probability-weighted value of expected future revenues associated with each underlying license. In developing such estimates, the Company applied judgment in determining the forecasted revenue, taking into consideration the applicable market conditions, the probability of success, and the time needed to develop each indication for which the license relates. The Company developed the estimated standalone selling price for the development services and clinical supply primarily based on the resources to be committed to perform the service. At inception of the contract, the Company allocated $ 17.4 million to the License Obligation, $ 20.8 million to the Development Services Obligation, $ 3.3 million to the Material Right Obligation and an immaterial amount to the Manufacturing Services Obligation. The License Obligation was satisfied in March 2025 upon transfer of the license to Kaken. For the Development Services Obligation, the Company recognizes revenue over time as Kaken consumes the benefit of such services as they are being performed. The Company measures proportional performance over time for the Development Services Obligation by using an input method based on cost incurred relative to the total estimated cost of the obligation on a quarterly basis. The Company re-evaluates the transaction price as uncertain events are resolved or other changes in circumstances occur as of the end of each reporting period. The Company recognized revenue of $ 17.4 million for the year ended December 31, 2025 related to the License Obligation and $ 6.7 million for the year ended December 31, 2025 related to the Development Services Obligation and Manufacturing Services Obligation. As of December 31, 2025, collaboration revenue receivable was less than $ 0.1 million, deferred revenue, current was $ 1.5 million and deferred revenue, non-current was $ 2.6 million. The aggregate estimated amount of transaction price that was unsatisfied as of December 31, 2025 was $ 17.6 million, of which, $ 14.3 million related to the Development Services Obligation that is expected to be recognized through 2028 as the Company performs its services towards the global development of envu in the dermatology field. The remaining $ 3.3 million estimated amount of transaction price that was unsatisfied as of December 31, 2025 related to the Material Right Obligation and is deferred until the option is exercised or expires. 143 Table of Contents ALUMIS INC. NOTES TO CONSOLIDATED FINANCIAL STATEMENTS Tenet Medicines Purchase Agreement In January 2024, ACELYRIN entered into an asset purchase agreement (“Purchase Agreement”) with Tenet Medicines, Inc. (“Tenet”). In consideration for the assets and other rights Tenet received under the Purchase Agreement, ACELYRIN is entitled to receive development, regulatory and commercial milestone payments of up to $ 157.5 million in the aggregate based on the achievement of specified milestones, royalties on worldwide net sales, and payments on sublicense income. On December 31, 2025, Climb Bio, Inc. (“Climb Bio”), the parent company of Tenet, filed a complaint in Delaware Superior Court seeking a declaratory judgment that budoprutug is not a “Product” under the Purchase Agreement, and therefore Climb Bio does not owe milestone or royalty payments to the Company under the Purchase Agreement. In January 2026, the Company issued a notice of material breach to Climb Bio for failing to timely pay a $ 3.0 million development milestone. The Company disputes Climb Bio’s interpretation and intends to seek recovery of the $ 3.0 million development milestone, as well as any other future milestone or royalty payments, through litigation. The matter remains pending. 8. Related Party Transactions Foresite Labs Services Agreement Foresite Labs, LLC (“Foresite Labs”) is an affiliate of Foresite Capital Management, a stockholder of the Company. In January 2021, the Company entered into a services agreement with Foresite Labs, which was amended and restated in August 2021 and in December 2023, and expires in December 2026, unless terminated earlier by the parties. Thereafter, on each anniversary of the effective date, the agreement will automatically renew for an additional one-year term, unless terminated earlier by the parties. Foresite Labs provides services to assist the Company in exploring specified immunology genetic targets. For the years ended December 31, 2025 and 2024, the Company recognized $ 1.1 million and $ 0.9 million as research and development expenses under the service agreement, respectively. Accrued expenses under the service agreement were zero as of December 31, 2025 and 2024. 9. Commitments and Contingent Liabilities Operating Leases In August 2022, the Company entered into a lease agreement for 55,000 square feet of office and laboratory space in South San Francisco, California, which commenced in January 2023 and has a contractual termination date in August 2033. The lease agreement includes a renewal option allowing the Company to extend this lease for an additional three years at the prevailing rental rate, which the Company was not reasonably certain to exercise. In December 2024, the Company entered into a lease agreement for approximately 22,000 square feet of additional office space in South San Francisco, California. The lease has a contractual termination date of December 2026, with the right to extend the lease for an additional two years subject to certain conditions. The Company determined that, for accounting purposes, the commencement date of the lease is in January 2025 and the lease term ends in December 2026, as it was not reasonably certain that the lease would be extended. As of the commencement date, future lease payments totaled $ 1.9 million and the lease liability was calculated to be $ 1.8 million, which is equal to the present value of the future lease payments, discounted at an incremental borrowing rate of 7.9 %. Upon the closing of the ACELYRIN Merger, the Company became the successor to ACELYRIN’s rights under ACELYRIN’s lease and sublease agreements. In January 2023, ACELYRIN entered into a lease agreement to rent approximately 10,012 square feet of office space in Southern California. The term of the lease is 65 months with an option to extend it for an additional three years . Monthly rent payments are approximately $ 30,500 , subject to an annual 3.0 % increase. In addition to the base rent, the Company is obligated to pay variable costs related to its share of operating expenses and taxes. In December 2025, the Company entered into an agreement to sublease the entirety of its Southern California leased space through August 24, 2028, the remainder of the lease term. The sublease included the operating lease right-of-use asset and certain property, plant and equipment. Sublease income was immaterial for the year ended 144 Table of Contents ALUMIS INC. NOTES TO CONSOLIDATED FINANCIAL STATEMENTS December 31, 2025. In July 2023, ACELYRIN entered into a lease agreement to rent approximately 22,365 square feet of office space in South San Francisco, California. The term of the lease is 60 months with an option to extend it for an additional five years . Monthly base rent payments are approximately $ 150,000 , subject to an annual 3.5 % increase. In February 2025, ACELYRIN entered into an agreement to sublease the entirety of its South San Francisco leased space through October 2029, the remainder of the lease term. The sublease included the operating lease right-of-use asset and certain property, plant and equipment. Sublease income was immaterial for the year ended December 31, 2025. The components of lease costs were as follows (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year Ended December 31, ​ ​ ​ ​ 2025 ​ ​ ​ 2024 Operating lease costs ​ $ 4,995 ​ $ 3,469 Variable lease costs ​ 1,312 ​ 1,202 Total lease costs ​ $ 6,307 ​ $ 4,671 ​ Supplemental cash flow information related to the operating leases were as follows (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ Year Ended December 31, ​ ​ 2025 ​ 2024 Cash payments included in the measurement of operating lease liabilities ​ $ 7,079 ​ $ 5,299 ​ Weighted-average remaining lease term and incremental borrowing rate for the operating leases were as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, ​ December 31, ​ ​ ​ ​ ​ 2025 ​ ​ ​ 2024 ​ Weighted-average remaining lease term (years) 6.8 ​ 8.7 ​ Weighted-average incremental borrowing rate 11.6 % 11.4 % ​ Future minimum lease payments under non-cancelable leases as of December 31, 2025 were as detailed below (in thousands): ​ ​ ​ ​ 2026 ​ $ 8,486 2027 ​ ​ 7,648 2028 ​ 7,765 2029 ​ 7,205 2030 ​ 5,848 Thereafter ​ 16,009 Total undiscounted lease payments ​ 52,961 Less: Imputed interest ​ ( 16,047 ) Total operating lease liabilities ​ $ 36,914 ​ FronThera Contingent Consideration In March 2021, the Company entered into the FronThera Acquisition, and the transaction was accounted for as an asset acquisition. Under the stock purchase agreement, the Company is obligated to pay contingent consideration of up to an aggregate of $ 120.0 million based on the achievement of specified clinical and approval milestones, including receipt of first commercialization approval in the United States or certain other jurisdictions, of up to an aggregate of $ 70.0 million payable for clinical milestones, and of up to an aggregate of $ 50.0 million payable for approval milestones, all related to technology acquired under the agreement. In the year ended December 31, 2022, the Company incurred and made a $ 37.0 million milestone payment for the first administration of envu to a patient enrolled in a Phase 2 clinical trial of envu, which 145 Table of Contents ALUMIS INC. NOTES TO CONSOLIDATED FINANCIAL STATEMENTS was recorded in research and development expenses in the consolidated statements of operations and comprehensive loss. In July 2024, the Company met a milestone in connection with the first administration of envu to a patient enrolled in a Phase 3 clinical trial of envu and made a $ 23.0 million milestone payment in August 2024, which was recorded in research and development expenses in the consolidated statements of operations and comprehensive loss for the year ended December 31, 2024. No other milestones were achieved or were probable of being achieved as December 31, 2025. License and Commercialization Agreement with Pierre Fabre Upon the closing of the ACELYRIN Merger, the Company became the successor to ACELYRIN’s rights under the March 25, 2021 license and commercialization agreement with Pierre Fabre Medicament SAS (“Pierre Fabre”), as amended (the “Pierre Fabre Agreement”), through which ACELYRIN received certain exclusive worldwide licenses with the right to sublicense certain patents, know-how and other intellectual property to develop, manufacture, use and commercialize lonigutamab for non-oncology therapeutic indications. The license from Pierre Fabre extends to any product containing lonigutamab (excluding any fragments or derivatives) as its sole active ingredient (each, a “PF Licensed Product”). The Pierre Fabre Agreement prohibits the Company from using the licensed intellectual property in any antibody drug conjugate, multi-specific antibodies or any other derivatives of lonigutamab. The Company is obligated to (i) make payments of up to $ 100.5 million upon the achievement of various development and regulatory milestones, (ii) make milestone payments of up to $ 390.0 million upon the achievement of certain commercial milestones, and (iii) pay tiered royalties in the high single-digit to low-teen percentages to Pierre Fabre on worldwide net sales in a given calendar year. Royalties will be payable for each PF Licensed Product in a given country during a period commencing upon the first commercial sale of such PF Licensed Product in such country and continuing until the latest of (a) 10 years after such first commercial sale, (b) expiration of last-to-expire valid claim in a licensed patent in such country and (c) expiration of regulatory exclusivity for such PF Licensed Product in such country. In the event the Company enters into a sublicense with a third party, the Company must also share with Pierre Fabre a percentage of any revenues from option fees, upfront payments, license maintenance fees, milestone payments or the like generated from the sublicense. Such percentage may be between the high single-digits to the low thirties based on which stage of development of a PF Licensed Product the sublicense relates to. Unless earlier terminated, the Pierre Fabre Agreement will continue on a PF Licensed Product-by-PF Licensed Product and country-by-country basis until there are no more royalty payments owed to Pierre Fabre on any PF Licensed Product thereunder. Either party may terminate the Pierre Fabre Agreement upon an uncured material breach, or upon the bankruptcy or insolvency of the other party. Pierre Fabre may also terminate the agreement if the Company or any of its affiliates institutes a patent challenge against the licensed patents from Pierre Fabre. The Company may also terminate the Pierre Fabre Agreement with or without cause upon nine months ’ prior written notice, so long as there is no ongoing clinical trial for any PF Licensed Product. As of December 31, 2025, no milestones were probable and accrued in the consolidated balance sheets. Purchase Commitments The Company enters into various agreements in the ordinary course of business, such as those with suppliers, CROs , CMOs and clinical trial sites. Upon the closing of the ACELYRIN Merger, the Company became the successor to contracts with non-cancellable commitments under ACELYRIN contracts. The total value of non-cancellable purchase commitments under contracts was $ 1.6 million as of December 31, 2025. This presentation of non-cancellable purchase commitments does not include any estimates of potential reduction of such liabilities related to mitigation obligations of the counterparties in the event of cancellation under the terms of its engagements. Legal Contingencies From time to time, the Company has and may become involved in legal proceedings arising in the ordinary course of business, any or all of which could have a material adverse impact on the Company, including its financial position. The 146 Table of Contents ALUMIS INC. NOTES TO CONSOLIDATED FINANCIAL STATEMENTS outcomes of legal proceedings are not within the Company’s complete control and may not be known for prolonged periods of time. The Company records a liability for such matters when it is probable that future losses will be incurred and that such losses can be reasonably estimated. Significant judgment by the Company is required to determine both probability and the estimated amount. Legal costs related to these matters, including attorney fees, are expensed as incurred and are recorded as general and administrative expenses in the consolidated statements of operations and comprehensive loss. On November 15, 2023, a purported federal securities class action lawsuit was commenced in the United States District Court for the Central District of California. On February 15, 2024, the Court appointed joint lead plaintiffs and lead counsel. An amended complaint was filed on March 26, 2024 (Boukadoum v. Acelyrin, Inc. et al., No. 2:23-cv-09672-FMO-MAA), naming ACELYRIN and then-current and former executive officers and directors as defendants. The complaint alleges that the defendants violated the Exchange Act and Securities Act by misleading investors about the Phase 2b trial of izokibep in hidradenitis suppurativa. The original complaint was filed following ACELYRIN’s announcement of the week 16 results from the Part B portion of such Phase 2b trial. The amended complaint seeks damages and an award of reasonable costs and expenses, including attorneys’ fees, expert fees and other costs, as well as such other and further relief as the court may deem just and proper. On May 3, 2024, the defendants filed their motion to dismiss the amended complaint, which was granted by the court, with leave to amend, in January 2026. On February 5, 2026, the plaintiffs filed a second amended complaint, which seeks damages and an award of reasonable costs and expenses, as well as such other and further relief as the court may deem just and proper. On February 19, 2026, the defendants filed their motion to dismiss the second amended complaint, which remains pending. It is possible that additional suits will be filed, or allegations made by stockholders, with respect to these same or other matters and also naming the Company and/or its officers and directors as defendants. This lawsuit and any other potential lawsuits are subject to inherent uncertainties, and the actual defense and disposition costs will depend upon many unknown factors. The outcome of this lawsuit is necessarily uncertain. The Company could be forced to expend significant resources in the defense against this and any other related lawsuits and the Company may not prevail. The Company currently is not able to estimate the possible loss to the Company from this lawsuit, as this lawsuit is currently at an early stage, and such amounts could be material to the Company’s financial statements even if the Company prevails in the defense against this lawsuit. The Company cannot be certain how long it may take to resolve this lawsuit or the possible amount of any damages that the Company may be required to pay. As of December 31, 2025, the Company did not consider any payment to be probable or reasonably estimable and had not accrued for any potential liability relating to this lawsuit. 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. Its exposure under these agreements is unknown because it involves claims that may be made against the Company in the future. To the extent permitted under Delaware law, the Company has agreed to indemnify its directors and officers for certain events or occurrences while the director or officer is, or was serving, at a request in such capacity. To date, the Company has not paid any claims or been required to defend any action related to its indemnification obligations. As of December 31, 2025 and 2024, the Company did not have any material indemnification claims that were probable or reasonably possible and consequently has not recorded related liabilities. 10. Redeemable Convertible Preferred Stock In March 2024, the Company issued and sold an aggregate of 41,264,891 shares of Series C redeemable convertible preferred stock for gross proceeds of $ 129.5 million and incurred $ 0.4 million of offering costs. The purchase price for Series C redeemable convertible preferred stock was $ 3.13826 per share. Under the Series C stock purchase agreement, any time prior to the earliest of (i) December 31, 2024, (ii) the execution of a letter of intent for the sale of the Company, or (iii) the closing date of the Company’s IPO, at the discretion of the Company’s board of directors, the Company was obligated to sell and each Series C purchaser was obligated to purchase additional shares of Series C redeemable convertible preferred stock with the amount equal to the purchaser’s aggregate purchase price in the first tranche Series C closing less any previous payments by the purchaser as part of the Put Right (as defined below) exercise. If the purchaser did not purchase its full share in the second tranche closing (the “Second Tranche Series C Closing”), all of its existing 147 Table of Contents ALUMIS INC. NOTES TO CONSOLIDATED FINANCIAL STATEMENTS shares of Series C redeemable convertible stock and Series C-1 redeemable convertible preferred stock were convertible into voting common stock at a 10 -to-1 basis. Additionally, a purchaser had a right to purchase shares of Series C-1 redeemable convertible preferred stock at a purchase price of $ 4.00 per share beginning from the earlier of (a) September 4, 2024 or (b) the date of a significant partnering or collaboration agreement and expiring upon the earlier of (a) December 31, 2024, (b) the public filing of a registration statement on Form S-1 for the IPO, (c) the Second Tranche Series C Closing and (d) the execution of a letter of intent for the sale of the Company (the “Put Right”). The Put Right could only be exercised once. The Company determined that the Second Tranche Series C Closing and the Put Right were two freestanding financial instruments and recognized the derivative liabilities at their estimated fair value of $ 8.9 million at the issuance date. In May 2024, the Company closed the Second Tranche Series C Closing and issued an additional 41,264,892 shares of Series C redeemable convertible preferred stock at a price of $ 3.13826 per share. The Company received gross proceeds of $ 129.5 million and incurred $ 0.2 million of offering costs. Accordingly, the derivative liabilities were settled, and the Company reclassified the derivative liabilities, remeasured at fair value of $ 14.3 million, into redeemable convertible preferred stock. Immediately prior to the closing of the Company’s IPO on July 1, 2024, all outstanding shares of the Company’s redeemable convertible preferred stock were converted and then redesignated into voting and non-voting common stock and are no longer outstanding. ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ 11. Stockholders’ Equity (Deficit) As of December 31, 2023, the Company was authorized to issue 125,000,000 shares of Class A common stock and 85,960,088 shares of Class B common stock, both with par values of $ 0.0001 per share. In June 2024, the Company’s board of directors approved the amended and restated certificate of incorporation, which was filed upon the closing of the IPO and which authorized the Company to issue up to 50,000,000 shares of preferred stock, with a par value of $ 0.0001 per share, and 492,815,092 shares of voting common stock and 7,184,908 shares of non-voting common stock, both with par values of $ 0.0001 per share. 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 to 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. 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 voting common stock and non-voting common stock, respectively. As of December 31, 2025, there were no shares of preferred stock issued or outstanding, and 99,084,365 and 5,622,408 shares of voting common stock and non-voting common stock, respectively, outstanding. The holders of voting and non-voting common stock have the same rights except that non-voting common stock does not have voting rights, except as may be required by law. Each holder of non-voting common stock has a right to convert each share of non-voting common stock to one share of voting common stock subject to the following limitations. At any time following the Company’s registration of any class of equity securities under the Exchange Act, the holders of shares of non-voting common stock may not convert a number of shares of non-voting common stock into shares of voting common stock in excess of that number of shares of non-voting common stock which would cause the holder thereof to beneficially own (for purposes of Section 13(d) of the Exchange Act), in excess of 4.99 % of the total number of issued and outstanding shares of voting common stock. Such maximum percentage may be increased or decreased to such other percentage as any holder of outstanding shares of non-voting common stock may designate in writing (in the case of an increase upon 61 days ’ prior written notice). 148 Table of Contents ALUMIS INC. NOTES TO CONSOLIDATED FINANCIAL STATEMENTS Common stock reserved for issuance, on an as-converted basis, consisted of the following as of December 31, 2025 and 2024: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, ​ ​ ​ December 31, ​ ​ 2025 ​ 2024 Stock options issued and outstanding 20,353,098 9,458,788 RSUs issued and outstanding ​ 2,527,377 ​ — Shares available for grant under the 2024 Equity Incentive Plan ​ 597,112 ​ 6,893,517 Shares available for grant under the 2024 Employee Stock Purchase Plan ​ 805,334 ​ 650,000 Shares available for grant under the ACELYRIN, Inc. 2023 Equity Incentive Plan ​ 6,585,521 ​ — Shares available for grant under the 2024 Performance Option Plan ​ 200,208 ​ 92,800 Total 31,068,650 17,095,105 ​ Common Stock Issued to Executives In February 2021, the Company issued 100,532 shares of restricted common stock to two executives at a purchase price of $ 0.94 per share. The shares vested over a four-year period with a one-year cliff vesting. While the shares were unvested, the holders had voting and dividends rights and the Company had the right to repurchase unvested shares of common stock at the price paid by the holder in the event of termination of the holder’s continuous status as a service provider. The Company estimated the fair value of the restricted stock awards based on the fair value of common stock at the grant dates. The expense was recognized ratably over the vesting terms. The Company recognized less than $ 0.1 million of stock-based compensation expense related to restricted stock awards for each of the years ended December 31, 2025 and 2024. The following table summarizes the activity for the Company’s restricted common stock for the years ended December 31, 2025 and 2024: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Weighted- ​ ​ ​ ​ Average ​ ​ Number of ​ Grant Date ​ ​ Shares ​ Fair Value Unvested as of December 31, 2024 2,583 ​ $ 2.90 Vested ( 2,583 ) ​ $ 2.90 Unvested as of December 31, 2025 — ​ $ — ​ 12. Stock-Based Compensation 2021 Stock Plan In February 2021, the Company adopted the 2021 Stock Plan (the “2021 Plan”), which provided for stock awards to eligible employees, directors and consultants of the Company. Awards issuable under the 2021 Plan included incentive stock options (“ISOs”), non-statutory stock options (“NSOs”), RSUs and stock grants. Subsequent to the adoption of the 2024 Equity Incentive Plan (the “2024 EIP”) in June 2024, described below, no additional shares were available for issuance under the 2021 Plan, and any stock options granted under the 2021 Plan that were subsequently forfeited would be made available for issuance under the 2024 EIP. The terms of the 2021 Plan permit option holders to exercise options before their options are vested. The shares of common stock granted upon early exercise that have not yet vested are subject to repurchase by the Company in the event of termination of the holder’s continuous status as a service provider, at the price paid by the holder. Stock Option Repricing In March 2024, the Company’s board of directors approved the repricing of all outstanding options as of March 29, 2024, which had an exercise price exceeding $ 8.84 per share. The exercise price of outstanding options with a weighted average 149 Table of Contents ALUMIS INC. NOTES TO CONSOLIDATED FINANCIAL STATEMENTS exercise price of $ 10.23 for 4,603,443 common stock shares was reduced to the estimated common stock fair value of $ 8.84 per share at the date of the repricing. The vesting terms and expiration dates remain unchanged from the original grant dates. The stock option repricing was treated as an option modification for accounting purposes and resulted in total incremental expense of $ 0.7 million, of which $ 0.1 million incremental expense associated with the vested options was recognized on the modification date. The remaining $ 0.6 million incremental expense associated with the unvested options as of the modification date is being recognized over the remainder of the original requisite service period. 2024 Performance Option Plan In May 2024, the Company’s board of directors adopted, and its stockholders approved, the 2024 Performance Option Plan (the “2024 POP”). The Company reserved 1,880,680 shares of common stock issuable under the 2024 POP. The 2024 POP permits grants of ISOs, NSOs and restricted stock awards to the Company’s employees, directors and consultants. In May 2024, the Company granted NSOs to employees to purchase 1,880,680 shares of common stock at an exercise price of $ 10.19 under the 2024 POP. Options generally vest on the date when the Company meets certain common stock public market price specified targets after the end of the IPO lock-up period, subject to continuous service through each respective vest date. The price targets are calculated based on the volume weighted average price per share over 30 consecutive trading dates, in accordance with the grant terms. The unvested awards will expire if it is determined that the vesting conditions have not been met during the applicable six-year performance period. The service condition includes monthly vesting over 36 months from the vesting commencement date and the employee’s continuous service with the Company through each such monthly vesting date. The terms of the 2024 POP permit option holders to exercise options before their options are vested, if the market condition has been met. 2024 Equity Incentive Plan In June 2024, the Company’s board of directors adopted, and its stockholders approved, the 2024 EIP, which became effective on June 27, 2024, upon execution of the underwriting agreement related to the Company’s IPO. The Company reserved 7,800,000 new shares of common stock for issuance under the 2024 EIP. In addition, up to 6,829,339 shares subject to awards under the 2021 Plan that terminate, expire, or lapse for any reason without the delivery of shares, or are reacquired or withheld (or not issued) to satisfy a tax withholding obligation or the purchase or exercise price, were authorized to be added to the 2024 EIP. The 2024 EIP also provides that the number of shares initially reserved and available for issuance will automatically increase each January 1, beginning on January 1, 2025 through January 1, 2034, by an amount equal to 5 % of the outstanding number of shares of the Company’s common stock as of the last day of the immediately preceding fiscal year, or such lesser number of shares as determined by the board of directors prior to the applicable January 1. Pursuant to this evergreen provision, the Company increased the number of shares reserved under the 2024 EIP by 2,720,366 on January 1, 2025. No more than 43,888,017 shares of common stock may be issued upon the exercise of incentive stock options under the 2024 EIP. The 2024 EIP allows the Company to make equity-based awards to its officers, employees, directors and consultants. The 2024 EIP provides for the grant of ISOs, NSOs, restricted stock awards, RSUs, stock appreciation rights, performance awards and other stock-based awards. Options under the 2024 EIP may be granted for periods of up to 10 years at exercise prices no less than the fair market value of common stock on the date of grant; provided, however, that the exercise price of an incentive stock option granted to a 10% stockholder may not be less than 110 % of the fair market value of the shares on the date of grant and such option may not be exercisable after the expiration of five years from the date of grant. Stock option grants under the 2024 EIP generally vest over four years . The grant date fair market value of all awards made under the 2024 EIP and all cash compensation paid by the Company to any non-employee director for services as a director in any fiscal year may not exceed $ 750,000 , increased to $ 1,000,000 in the fiscal year of their initial service as a non-employee director. The terms of the 2024 EIP do not permit option holders to exercise options before their options are vested. 150 Table of Contents ALUMIS INC. NOTES TO CONSOLIDATED FINANCIAL STATEMENTS ACELYRIN Plans Pursuant to the Merger Agreement, the Company assumed certain stock options, RSUs and performance RSUs outstanding under the ACELYRIN, Inc. 2020 Stock Option and Grant Plan, as amended (the “ACELYRIN 2020 Plan”), the ValenzaBio, Inc. Stock Plan (the “ValenzaBio Plan”) and the ACELYRIN, Inc. 2023 Equity Incentive Plan (the “ACELYRIN 2023 Plan” and, together with the ACELYRIN 2020 Plan and the ValenzaBio Plan, the “ACELYRIN Plans”). In connection with the closing of the ACELYRIN Merger, the Company also assumed the ACELYRIN 2023 Plan, which, as modified in connection with such assumption, permits equity awards to be issued to the extent permissible under applicable law and Nasdaq listing rules. Stock options that were outstanding under the ACELYRIN Plans immediately prior to the Closing Date were assumed by the Company and converted into options to purchase the Company’s common stock. RSUs that were outstanding and unvested immediately prior to the Closing Date were assumed by the Company and converted into the Company’s RSU awards. Performance RSUs outstanding and unvested immediately prior to the Closing Date were converted into the Company’s RSU awards subject only to a service vesting condition. Stock Option Activity The following table summarizes the Company’s stock option activity, excluding under the 2024 POP, for the year ended December 31, 2025 and includes early exercised shares as part of stock options exercised: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Weighted- ​ ​ ​ ​ ​ ​ ​ Weighted- ​ Average ​ ​ ​ ​ ​ ​ ​ Average ​ Remaining ​ Aggregate ​ ​ ​ ​ ​ ​ ​ ​ Exercise ​ ​ ​ Contractual ​ ​ ​ Intrinsic ​ ​ ​ ​ Price Per ​ Term ​ Value ​ ​ Options ​ Share ​ (in years) ​ (in thousands) Outstanding as of December 31, 2024 7,670,908 ​ $ 9.59 8.2 ​ $ 1,777 Stock options assumed in connection with the ACELYRIN Merger ​ 4,712,186 ​ $ 12.99 ​ ​ ​ ​ ​ Granted 7,465,188 ​ $ 4.77 ​ ​ ​ ​ ​ Exercised ( 57,659 ) ​ $ 8.71 ​ ​ ​ $ 138 Forfeited or expired ( 1,117,997 ) ​ $ 9.11 ​ ​ ​ ​ ​ Outstanding, vested and expected to vest as of December 31, 2025 18,672,626 ​ $ 8.56 ​ 6.7 ​ $ 44,015 Exercisable as of December 31, 2025 ​ 10,844,789 ​ $ 10.68 ​ 4.9 ​ $ 9,020 ​ Total exercisable shares of 10,844,789 as of December 31, 2025 included 1,975,031 unvested shares that were early exercisable under the 2021 Plan. The total fair value of stock options vested during the years ended December 31, 2025 and 2024 was $ 27.0 million and $ 5.8 million, respectively. 151 Table of Contents ALUMIS INC. NOTES TO CONSOLIDATED FINANCIAL STATEMENTS The following table summarizes the Company’s stock option activity under the 2024 POP for the year ended December 31, 2025. ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Weighted- ​ ​ ​ ​ ​ ​ ​ ​ ​ Weighted- ​ Average ​ ​ ​ ​ ​ ​ ​ Average ​ Remaining ​ Aggregate ​ ​ ​ ​ Exercise ​ Contractual ​ Intrinsic ​ ​ ​ ​ Price Per ​ Term ​ Value ​ ​ Options ​ Share ​ (in years) ​ (in thousands) Outstanding as of December 31, 2024 1,787,880 ​ $ 10.19 ​ 9.3 ​ $ — Granted — ​ $ — ​ ​ ​ ​ Forfeited or expired ( 107,408 ) ​ $ 10.19 ​ ​ ​ ​ Outstanding, vested and expected to vest as of December 31, 2025 1,680,472 ​ $ 10.19 ​ 8.3 ​ $ — Exercisable as of December 31, 2025 — ​ $ — ​ — ​ $ — ​ Valuation of Stock Options Granted under Non-Performance Plans The weighted-average grant date fair value of stock options granted for the years ended December 31, 2025 and 2024 was $ 3.86 and $ 9.92 per stock option, respectively. The fair value of stock options granted for the years ended December 31, 2025 and 2024, was estimated using the Black-Scholes option pricing model with the following assumptions: ​ ​ ​ ​ ​ ​ ​ ​ Year Ended December 31, ​ ​ ​ ​ 2025 ​ ​ ​ 2024 Expected term (in years) ​ 5.2 - 6.1 5.8 - 6.1 Volatility ​ 98.84 % - 104.32 % 103.65 % - 109.78 % Risk-free interest rate ​ 3.69 % - 4.65 % 3.47 % - 4.48 % Dividend yield ​ 0.00 % ​ 0.00 % ​ Expected Term ​ The expected term represents the weighted-average period the stock options are expected to remain outstanding and is based on the options’ vesting terms and contractual terms as the Company does not have sufficient historical information to develop reasonable expectations about future exercise patterns and post-vesting employment termination behavior. Expected Volatility The expected stock price volatility assumption was determined by examining the historical volatilities for industry peers, as the Company did not have sufficient trading history of its common stock. The Company will continue to use industry peers in determining historical stock price volatility until sufficient historical data of its common stock becomes available. Risk-Free Interest Rate The risk-free interest rate assumption is based on the U.S. Treasury instruments whose term was consistent with the expected term of the Company’s stock options. Dividends The Company has not paid any cash dividends on common stock since inception and does not anticipate paying any dividends in the foreseeable future. Consequently, an expected dividend yield of zero was used. 152 Table of Contents ALUMIS INC. NOTES TO CONSOLIDATED FINANCIAL STATEMENTS Valuation of Stock Options Granted under the 2024 POP ​ Stock options granted under the 2024 POP vest based on service, market and performance conditions (the occurrence of the IPO or a change of control) and are classified as equity financial instruments. At the grant date, the fair value of stock options granted under the 2024 POP was estimated using a Monte Carlo simulation model, which uses a distribution of potential outcomes on a monthly basis over the vesting period prioritizing the most reliable information available. The assumptions utilized in the calculation were based on the achievement of certain stock price thresholds, including the Company’s expected common stock price, expected volatility, risk-free rate and expected term. The Company used the following assumptions to estimate the fair value at the grant date in May 2024: common stock fair value of $ 12.06 , vesting term of 6.0 years, volatility of 122.00 %, and risk-free rate of 4.38 %. The estimates of fair value are uncertain and changes in any of the estimated inputs could have resulted in significant adjustments to the fair value. ​ The Company’s estimated fair value of stock options issued under the 2024 POP of $ 18.0 million is recognized using graded vesting from July 1, 2024, the closing of the IPO, when the performance condition was met, over the longer of (i) the explicit service period of the service condition of 36 months or (ii) the derived service period between 1.4 years to 2.1 years, as determined for each graded vesting tranche. Early Exercise of Employee Stock Options Proceeds from the early exercise of stock options are recorded as share repurchase liability, and as shares vest are recognized to additional paid-in capital in the consolidated balance sheets. As of December 31, 2025 and 2024, there was $ 0.1 million and $ 0.8 million share repurchase liability related to unvested shares, respectively, classified as share repurchase liability in the consolidated balance sheets. The following table summarizes the activity for the Company’s early exercised shares for the years ended December 31, 2025 and 2024: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Weighted- ​ ​ ​ ​ Average ​ ​ Number of ​ Exercise Price ​ ​ ​ ​ Shares ​ ​ ​ Per Share Unvested as of December 31, 2023 327,100 ​ $ 5.33 Early exercised 25,034 ​ $ 8.84 Vested ( 205,451 ) ​ $ 5.62 Unvested as of December 31, 2024 146,683 ​ $ 5.53 Early exercised — ​ $ — Vested ( 133,002 ) ​ $ 5.17 Unvested as of December 31, 2025 13,681 ​ $ 9.01 ​ 2024 Employee Stock Purchase Plan ​ In June 2024, the Company’s board of directors adopted, and its stockholders approved, the 2024 ESPP, which became effective on June 28, 2024, upon execution of the underwriting agreement related to the Company’s IPO. The Company initially reserved 650,000 shares of common stock for issuance under the 2024 ESPP. The number of shares of common stock reserved for issuance under the 2024 ESPP will be automatically increased each year for ten calendar years beginning on January 1, 2025 through January 1, 2034, by the lesser of (i) 1 % of the total number of shares of our common stock outstanding on the last day of the calendar month before the date of the automatic increase, and (ii) 1,950,000 shares; provided that before the date of any such increase, the board of directors may determine that such increase will be less than the amount in (i) and (ii) above. Pursuant to this evergreen provision, the Company increased the number of shares reserved under the 2024 ESPP by 544,073 on January 1, 2025. The 2024 ESPP allows an eligible employee to purchase shares of common stock at an amount equal to 85 % of the lower of the fair market value of the Company’s common stock at the beginning of the offering period or at each applicable purchase date during an offering period as established by the 153 Table of Contents ALUMIS INC. NOTES TO CONSOLIDATED FINANCIAL STATEMENTS board of directors. The first purchase period commenced on January 24, 2025 and ended on May 20, 2025. During the year ended December 31, 2025, 388,739 shares of common stock were purchased under the 2024 ESPP. ​ The following table summarizes the Black-Scholes option pricing model used in estimating the fair value of the stock purchase rights under the 2024 ESPP for the year ended December 31, 2025: ​ ​ ​ ​ ​ ​ Year Ended ​ ​ ​ ​ December 31, 2025 Expected term (in years) ​ 0.3 - 0.5 Volatility ​ 67.54 % - 133.00 % Risk-free interest rate ​ 3.75 % - 4.33 % Dividend yield ​ 0.00 % ​ Restricted Stock Units A summary of unvested RSU activity for the year ended December 31, 2025 is presented in the following table: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Weighted- ​ ​ ​ ​ Average ​ ​ ​ ​ Grant Date ​ ​ Number of ​ Fair Value ​ ​ ​ ​ Shares ​ ​ ​ Per Share RSUs assumed in connection with the ACELYRIN Merger 1,470,868 ​ $ 4.78 RSUs granted 2,456,475 ​ $ 3.95 RSUs released ​ ( 1,201,282 ) ​ $ 4.78 RSUs forfeited ( 198,684 ) ​ $ 4.24 Unvested as of December 31, 2025 2,527,377 ​ $ 4.01 ​ Stock-Based Compensation Expense The following table summarizes stock-based compensation expense recognized in the Company’s consolidated statements of operations and comprehensive loss for the years ended December 31, 2025 and 2024 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ Year Ended December 31, ​ ​ ​ ​ 2025 ​ ​ ​ 2024 Research and development ​ $ 21,305 ​ $ 10,110 General and administrative ​ ​ 22,219 ​ ​ 9,347 Total stock-based compensation expense ​ $ 43,524 ​ $ 19,457 ​ Stock-based compensation expense included $ 9.0 million as general and administrative expenses and $ 4.1 million as research and development expenses for the year ended December 31, 2025, related to accelerated vesting and exercise term modification for severed employees in connection with the ACELYRIN Merger. 154 Table of Contents ALUMIS INC. NOTES TO CONSOLIDATED FINANCIAL STATEMENTS The following table summarizes the stock-based compensation expense recognized in the Company’s consolidated statements of operations and comprehensive loss by award type for the years ended December 31, 2025 and 2024 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ Year Ended December 31, ​ ​ ​ ​ 2025 ​ ​ ​ 2024 Stock options ​ $ 35,861 ​ $ 19,399 RSUs ​ ​ 6,678 ​ ​ — ESPP ​ ​ 979 ​ ​ — Restricted stock awards ​ ​ 6 ​ ​ 58 Total stock-based compensation expense ​ $ 43,524 ​ $ 19,457 ​ Stock-based compensation expense related to non-employee awards was $ 0.8 million and $ 0.3 million for the years ended December 31, 2025 and 2024, respectively. The Company recognized $ 7.4 million and $ 5.7 million in stock-based compensation expense related to the 2024 POP for the years ended December 31, 2025 and 2024. As of December 31, 2025, there was unrecognized stock-based compensation expense of $ 60.0 million related to unvested stock options and RSUs which the Company expects to recognize over a remaining weighted-average period of 2.58 years. 13. Employee Benefit Plans The Company sponsors a qualified 401(k) defined contribution plan covering eligible employees. Participants may contribute a portion of their annual compensation limited to a maximum annual amount set by the Internal Revenue Service. There were no employer contributions under this plan for the years ended December 31, 2025 and 2024. In November 2025, the Company’s board of directors approved a Company match of 100 % of participating employees’ deferral contribution up to 3 % of eligible compensation and a 50 % match of participating employees’ deferral contribution from 3 % to 5 % of eligible compensation, effective from January 1, 2026. 14. Net Loss Per Share Attributable to Common Stockholders The following table presents the computation of the basic and diluted net loss per share attributable to common stockholders for the years ended December 31, 2025 and 2024 (in thousands, except share and per share amounts): ​ ​ ​ ​ ​ ​ ​ ​ ​ Year Ended December 31, ​ ​ ​ ​ 2025 ​ ​ ​ 2024 Numerator: ​ ​ ​ ​ ​ ​ Net loss ​ $ ( 243,325 ) ​ $ ( 294,233 ) Denominator: ​ ​ ​ ​ Weighted-average shares of common stock outstanding ​ 85,096,243 ​ 28,579,979 Less: Weighted-average shares of common stock subject to repurchase ​ ( 66,619 ) ​ ( 238,113 ) Weighted-average shares of common stock outstanding, basic and diluted ​ ​ 85,029,624 ​ ​ 28,341,866 Net loss per share attributable to common stockholders, basic and diluted ​ $ ( 2.86 ) ​ $ ( 10.38 ) ​ 155 Table of Contents ALUMIS INC. NOTES TO CONSOLIDATED FINANCIAL STATEMENTS The following outstanding potentially dilutive securities were excluded from the computation of diluted net loss per share attributable to common stockholders for the periods presented, because including them would have been anti-dilutive (on an as-converted basis): ​ ​ ​ ​ ​ ​ ​ ​ December 31, ​ December 31, ​ ​ ​ ​ 2025 ​ ​ ​ 2024 Stock options issued and outstanding 20,353,098 9,458,788 RSUs issued and outstanding ​ 2,527,377 ​ — Common stock issuable under the 2024 ESPP ​ 264,360 ​ — Early exercised stock options and unvested restricted common stock 13,681 149,266 Total 23,158,516 9,608,054 ​ ​ ​ 15. Income Taxes Net loss before provision for income taxes distributed geographically was as follows for the years ended December 31, 2025 and 2024 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ Year Ended December 31, ​ ​ 2025 ​ 2024 Domestic ​ $ ( 251,886 ) ​ $ ( 294,233 ) Foreign ​ ​ — ​ ​ — Total ​ $ ( 251,886 ) ​ $ ( 294,233 ) ​ The provision for income taxes was as follows for the years ended December 31, 2025 and 2024 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year Ended December 31, ​ ​ 2025 ​ 2024 Current ​ ​ ​ ​ ​ ​ Federal ​ $ — ​ $ — State and local ​ ​ — ​ ​ — Foreign ​ ​ — ​ ​ — Total Current ​ $ — ​ $ — ​ ​ ​ ​ ​ ​ ​ Deferred ​ ​ ​ ​ ​ ​ Federal ​ $ ( 8,561 ) ​ $ — State and local ​ ​ — ​ ​ — Foreign ​ ​ — ​ ​ — Total Deferred ​ $ ( 8,561 ) ​ $ — ​ ​ ​ ​ ​ ​ ​ Total income tax provision (benefit) ​ $ ( 8,561 ) ​ $ — ​ 156 Table of Contents ALUMIS INC. NOTES TO CONSOLIDATED FINANCIAL STATEMENTS A reconciliation of the provision for income taxes to the amount computed by applying the 21 % statutory U.S. federal income tax rate to net loss before income taxes after the adoption of ASU 2023-09 is as follows (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year Ended December 31, 2025 ​ ​ ​ $ ​ % Net loss before income taxes ​ $ ( 251,886 ) ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ U.S. federal statutory tax rate ​ ​ ( 52,896 ) ​ 21.0 % State and local income taxes, net of federal effect (1) ​ ​ ( 3 ) ​ - % Tax credits ​ ​ ​ ​ ​ ​ Research and development credits ​ ​ 11,129 ​ ( 4.4 ) % Changes in valuation allowance ​ 64,966 ​ ( 25.8 ) % Nontaxable or nondeductible items ​ ​ ​ ​ ​ Nondeductible officer's compensation ​ ​ 593 ​ ( 0.2 ) % Gain on bargain purchase ​ ​ ( 39,461 ) ​ 15.7 % Stock-based compensation ​ 4,621 ​ ( 1.9 ) % Transaction costs ​ ​ 2,346 ​ ( 0.9 ) % Other ​ ​ 144 ​ ( 0.1 ) % Total ​ $ ( 8,561 ) ​ 3.4 % (1) The state and local tax effect in this category is not material to the consolidated financial statements. ​ A reconciliation of the provision for income taxes to the amount computed by applying the 21 % statutory U.S. federal income tax rate to net loss before income taxes for the year ended December 31 2024, prior to the adoption of ASU 2023-09, is as follows (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ Year Ended December 31, ​ ​ 2024 Amount at statutory tax rates ​ $ ( 61,789 ) Permanent differences ​ 3,000 Valuation allowance ​ 64,923 Stock-based compensation ​ 3,356 Federal research and development credit ​ ( 9,520 ) Other ​ 30 Total ​ $ — ​ The Company recognized a benefit from income taxes of $ 8.6 million for the year ended December 31, 2025. The income tax benefit is primarily related to the realization of deferred tax assets and valuation allowance release as a result of the ACELYRIN Merger. No provision for income taxes was recorded for the year ended December 31, 2024, as the Company operated with taxable losses. The Company has only incurred net operating losses in the United States since inception. On July 4, 2025, the One Big Beautiful Bill Act (the “OBBBA”) was enacted in the United States. The OBBBA includes significant provisions, including, but not limited to, modifications of capitalization of research and development expenses and accelerated fixed asset depreciation. The adoption of the OBBBA did not have a material impact on the Company’s consolidated financial statements for the year ended December 31, 2025. 157 Table of Contents ALUMIS INC. NOTES TO CONSOLIDATED FINANCIAL STATEMENTS Significant components of the deferred tax assets (liabilities) balances as of December 31, 2025 and 2024 were as follows (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, ​ ​ ​ December 31, ​ ​ 2025 ​ 2024 Deferred tax assets: ​ ​ ​ ​ ​ ​ Net operating losses ​ $ 59,420 ​ $ 21,573 Tax credits ​ 8,025 ​ 17,407 Research and development capitalization ​ 191,356 ​ 74,211 Fixed assets and intangibles ​ ​ 6,898 ​ ​ — Accruals and reserves ​ 2,002 ​ 115 Stock-based compensation ​ 7,559 ​ 3,088 Operating lease liabilities ​ 7,754 ​ 6,452 Other capitalized expenses ​ 14,160 ​ 11,832 Gross deferred tax assets ​ 297,174 ​ 134,678 Valuation allowance ​ ( 292,978 ) ​ ( 127,990 ) Deferred tax assets, net of valuation allowance ​ $ 4,196 ​ $ 6,688 Deferred tax liabilities: ​ ​ ​ ​ ​ ​ Fixed assets and intangibles ​ $ — ​ $ ( 885 ) Operating lease right-of-use assets ​ ( 6,336 ) ​ ( 5,803 ) Deferred tax liabilities ​ ( 6,336 ) ​ ( 6,688 ) Total net deferred tax assets ​ $ ( 2,140 ) ​ $ — ​ A valuation allowance is required to be established when it is more likely than not that all or a portion of a deferred tax asset will not be realized. Realization of deferred tax assets is dependent upon future earnings, the timing and amount of which are uncertain. The Company believes that, based on a number of factors such as the history of operating losses, it is more likely than not that the deferred tax assets will not be fully realized, such that a valuation allowance has been recorded. The valuation allowance increased by $ 165.0 million and by $ 66.6 million for the years ended December 31, 2025 and 2024, respectively, primarily due to capitalized research and development expenditures and net operating losses carryforwards. The following table presents the Company’s U.S. federal and state net operating loss carryforwards and tax credits as of December 31, 2025 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Amount ​ ​ ​ Begin to Expire Net operating losses, U.S. federal ​ $ 264,643 Do not expire Net operating losses, U.S. federal ​ $ 16,520 2037 Net operating losses, U.S. states ​ $ 5,866 2041 Tax credits, U.S. federal ​ $ 3,493 2045 Tax credits, U.S. states ​ $ 8,238 2037 ​ Utilization of some of the U.S. federal and state net operating loss and credit carryforwards may be subject to annual limitations due to the change in ownership provisions of the Internal Revenue Code and similar state provisions. The annual limitation may result in the expiration of net operating losses and credits before utilization. As of December 31, 2025, the Company has completed an Internal Revenue Code Section 382 analysis which resulted in the expiration of U.S. federal net credits before utilization and, as such, has recognized a reduction of deferred tax assets. As the Company has recognized a valuation allowance, any potential limitation is not expected to have a material impact to the consolidated financial statements. 158 Table of Contents ALUMIS INC. NOTES TO CONSOLIDATED FINANCIAL STATEMENTS Uncertain Tax Positions A reconciliation of the beginning and ending balances of the unrecognized tax benefits for the years ended December 31, 2025 and 2024, is as follows (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year Ended December 31, ​ ​ 2025 ​ 2024 Beginning balance ​ $ 2,797 ​ $ 4,116 Increases in tax positions in the current period ​ 1,164 ​ 1,336 Decreases related to prior year’s tax position ​ ( 1,985 ) ​ ( 2,655 ) Ending balance ​ $ 1,976 ​ $ 2,797 ​ The entire amount of the unrecognized tax benefits would not impact the Company’s effective tax rate if recognized. The Company has elected to include interest and penalties as a component of other income (expense), net. For the years ended December 31, 2025 and 2024, the Company did no t recognize any accrued interest and penalties related to unrecognized tax benefits. As of December 31, 2025, the Company is not under audit by the Internal Revenue Service or any state authority for income taxes for any open years. Due to the Company’s net operating loss carryforwards, the Company’s domestic income tax returns are open to examination by the Internal Revenue Service beginning with tax year 2017 and by state taxing authorities beginning with tax year 2021. Income Taxes Paid Disclosure (under ASU 2023-09) The amounts of cash income taxes paid by the Company for the years ended December 31, 2025 and 2024 were immaterial. 16. Segment Reporting For purposes of evaluating performance and allocating resources, the Company’s CODM, its Chief Executive Officer, regularly reviews consolidated net loss as reported in the Company’s consolidated statements of operations and comprehensive loss as compared to budget. The measure of segment assets is reported in the consolidated balance sheets as total consolidated assets. 159 Table of Contents ALUMIS INC. NOTES TO CONSOLIDATED FINANCIAL STATEMENTS In addition to the significant expense categories included within consolidated net loss presented in the Company’s consolidated statements of operations and comprehensive loss, see below for disaggregated amounts that comprise research and development expenses for the years ended December 31, 2025 and 2024 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year Ended December 31, ​ ​ ​ ​ ​ 2025 ​ ​ ​ 2024 Revenue: ​ ​ ​ ​ ​ ​ ​ License revenue ​ $ 17,389 ​ $ — ​ Collaboration revenue ​ ​ 6,661 ​ ​ — ​ Total revenue ​ ​ 24,050 ​ ​ — ​ Operating expenses: ​ ​ ​ ​ ​ ​ ​ Research and development expenses ​ ​ ​ ​ ​ ​ ​ External costs ​ ​ ​ ​ ​ ​ ​ Milestones related to previously acquired IPR&D assets ​ ​ — ​ ​ 23,000 ​ CROs, CMOs and clinical trials ​ ​ 231,118 ​ ​ 151,422 ​ Professional consulting services ​ ​ 30,157 ​ ​ 19,154 ​ Other research and development costs ​ ​ 9,096 ​ ​ 10,258 ​ Internal costs ​ ​ ​ ​ ​ ​ ​ Personnel-related costs ​ ​ 92,702 ​ ​ 46,774 ​ Facilities and overhead costs ​ ​ 22,925 ​ ​ 14,946 ​ Total research and development expense ​ ​ 385,998 ​ ​ 265,554 ​ General and administrative expenses ​ ​ 91,856 ​ ​ 35,200 ​ Total operating expenses ​ 477,854 ​ 300,754 ​ Loss from operations ​ ( 453,804 ) ​ ( 300,754 ) ​ Total other income (expense), net ​ 201,918 ​ 6,521 ​ Net loss before income taxes ​ ​ ( 251,886 ) ​ ​ ( 294,233 ) ​ Income tax benefit ​ ​ 8,561 ​ ​ — ​ Net loss ​ $ ( 243,325 ) ​ $ ( 294,233 ) ​ ​ ​ ​ 17. Subsequent Events On March 18, 2026, the Company entered into a Controlled Equity Offering SM Sales Agreement (the “Sales Agreement”) with Cantor as sales agent, pursuant to which the Company may offer and sell, from time to time through Cantor, at its option, shares of its common stock having an aggregate offering price of up to $ 300.0 million (the “ATM Shares”). The sales of the ATM Shares will be made by any method permitted that is deemed to be an “at-the-market” equity offering as defined in Rule 415(a)(4) promulgated under the Securities Act, including sales made directly on or through the Nasdaq Global Select Market. The Company agreed to pay Cantor a commission of up to 3.0 % of the aggregate gross proceeds from any ATM Shares sold by Cantor. ​ ​ 160 Table of Contents Item 9. Changes in and Disagreements with Accountants on Accounting and Financial Disclosure None.