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 ) 122 Consolidated Balance Sheets ​ 123 Consolidated Statements of Operations and Comprehensive Loss ​ 124 Consolidated Statements of Redeemable Convertible Preferred Stock and Stockholders’ Equity (Deficit) ​ 125 Consolidated Statements of Cash Flows ​ 126 Notes to Consolidated Financial Statements ​ 127 ​ ​ 121 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 2024 financial statements of Alumis Inc. and the 2023 consolidated financial statements of Alumis Inc. and its subsidiaries (collectively referred to as the “Company”), which comprise the balance sheets as of December 31, 2024 and 2023, and the related 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 “financial statements”). In our opinion, the financial statements present fairly, in all material respects, the financial position of the Company as of December 31, 2024 and 2023, 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. Substantial Doubt About the Company’s Ability to Continue as a Going Concern The accompanying financial statements have been prepared assuming that the Company will continue as a going concern. As discussed in Note 1 to the financial statements, the Company has incurred negative operating cash flows and significant losses from operations since its inception that raise substantial doubt about its ability to continue as a going concern. Management’s plans in regard to these matters are also described in Note 1. The financial statements do not include any adjustments that might result from the outcome of this uncertainty. Basis for Opinion These financial statements are the responsibility of the Company’s management. Our responsibility is to express an opinion on the Company’s 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 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 financial statements are free of material misstatement, whether due to error or fraud. Our audits included performing procedures to assess the risks of material misstatement of the 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 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 financial statements. We believe that our audits provide a reasonable basis for our opinion. /s/ PricewaterhouseCoopers LLP San Jose, California March 19, 2025 We have served as the Company’s auditor since 2022. ​ 122 Table of Contents ALUMIS INC. CONSOLIDATED BALANCE SHEETS ​ ​ ​ ​ ​ ​ ​ ​ December 31, December 31, (in thousands, except share and per share amounts) ​ 2024 ​ 2023 Assets ​ ​ Current assets: ​ ​ Cash and cash equivalents ​ $ 169,526 ​ $ 45,996 Restricted cash ​ — ​ 113 Marketable securities ​ 118,737 ​ 2,956 Research and development prepaid expenses ​ 13,424 ​ 2,661 Other prepaid expenses and current assets ​ 4,501 ​ 1,631 Total current assets ​ 306,188 ​ 53,357 Restricted cash, non-current ​ 1,106 ​ 1,024 Property and equipment, net ​ 20,968 ​ 22,441 Operating lease right-of-use assets, net ​ 12,723 ​ 12,783 Other long-term assets ​ 7 ​ 7 Total assets ​ $ 340,992 ​ $ 89,612 Liabilities, Redeemable Convertible Preferred Stock and Stockholders’ Equity (Deficit) ​ ​ Current liabilities: ​ ​ Accounts payable ​ $ 9,624 ​ $ 1,118 Research and development accrued expenses ​ 29,149 ​ 10,946 Other accrued expenses and current liabilities ​ 10,580 ​ 7,087 Operating lease liabilities, current ​ 1,557 ​ 1,720 Total current liabilities ​ 50,910 ​ 20,871 Operating lease liabilities, non-current ​ 29,165 ​ 30,860 Share repurchase liability ​ 813 ​ 1,771 Total liabilities ​ 80,888 ​ 53,502 Commitments and contingencies (Note 7) ​ ​ Redeemable convertible preferred stock, $ 0.0001 par value; zero and 89,016,578 shares authorized as of December 31, 2024 and 2023, respectively; zero and 85,960,088 shares issued and outstanding as of December 31, 2024 and 2023, respectively; aggregate liquidation preference of zero and $ 370,540 as of December 31, 2024 and 2023, respectively ​ — ​ 375,370 Stockholders’ equity (deficit): ​ ​ ​ Preferred stock, $ 0.0001 par value; 50,000,000 shares authorized, zero shares issued and outstanding as of December 31, 2024; zero shares authorized, issued and outstanding as of December 31, 2023 ​ ​ — ​ ​ — Common stock, voting, $ 0.0001 par value; 492,815,092 and 125,000,000 voting shares authorized as of December 31, 2024 and 2023, respectively; 47,222,419 and 2,675,979 voting shares issued and outstanding as of December 31, 2024 and 2023, respectively ​ 4 ​ 1 Common stock, non-voting, $ 0.0001 par value; 7,184,908 and 85,960,088 non-voting shares authorized as of December 31, 2024 and 2023, respectively; 7,184,908 and zero non-voting shares issued and outstanding as of December 31, 2024 and 2023, respectively ​ ​ 1 ​ ​ — Additional paid-in capital ​ 918,610 ​ 25,055 Accumulated other comprehensive income (loss) ​ 40 ​ 2 Accumulated deficit ​ ( 658,551 ) ​ ( 364,318 ) Total stockholders’ equity (deficit) ​ 260,104 ​ ( 339,260 ) Total liabilities, redeemable convertible preferred stock and stockholders’ equity (deficit) ​ $ 340,992 ​ $ 89,612 ​ The accompanying notes are an integral part of these consolidated financial statements. ​ 123 Table of Contents ALUMIS INC. CONSOLIDATED STATEMENTS OF OPERATIONS AND COMPREHENSIVE LOSS ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year Ended December 31, ​ (in thousands, except share and per share amounts) 2024 2023 Operating expenses: ​ ​ ​ ​ ​ ​ ​ Research and development expenses, including related party expenses of $ 912 and $ 1,519 for the years ended December 31, 2024 and 2023, respectively ​ $ 265,554 ​ $ 137,676 ​ General and administrative expenses ​ 35,200 ​ 20,498 ​ Total operating expenses ​ 300,754 ​ 158,174 ​ Loss from operations ​ ( 300,754 ) ​ ( 158,174 ) ​ Other income (expense): ​ ​ ​ Interest income ​ 12,020 ​ 3,368 ​ Change in fair value of derivative liability ​ ( 5,406 ) ​ ( 119 ) ​ Other income (expenses), net ​ ( 93 ) ​ ( 68 ) ​ Total other income (expense), net ​ 6,521 ​ 3,181 ​ Net loss ​ $ ( 294,233 ) ​ $ ( 154,993 ) ​ Other comprehensive income (loss): ​ ​ ​ Unrealized gain (loss) on marketable securities, net ​ 38 ​ 129 ​ Net loss and other comprehensive loss ​ $ ( 294,195 ) ​ $ ( 154,864 ) ​ Net loss per share attributable to common stockholders, basic and diluted ​ $ ( 10.38 ) ​ $ ( 72.08 ) ​ Weighted-average shares of common stock outstanding, basic and diluted ​ 28,341,866 ​ 2,150,186 ​ ​ The accompanying notes are an integral part of these consolidated financial statements. ​ 124 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, 2022 67,960,088 ​ $ 285,473 ​ 2,642,334 ​ $ 1 ​ $ 14,209 ​ $ ( 127 ) ​ $ ( 209,325 ) ​ $ ( 195,242 ) Issuance of Series B-2 and B-2A redeemable convertible preferred stock in May 2023 for cash, net of derivative liability of $ 2,112 and offering costs of $ 208 12,000,000 ​ 57,679 ​ — ​ — ​ — ​ — ​ — ​ — Issuance of Series B-2 and B-2A redeemable convertible preferred stock in October 2023 for cash, net of offering costs of $ 13 , and settlement of derivative liability of $ 2,231 6,000,000 ​ 32,218 ​ — ​ — ​ — ​ — ​ — ​ — Issuance of common stock upon exercise of stock options and early exercise of stock options — ​ — ​ 48,442 ​ — ​ 277 ​ — ​ — ​ 277 Vesting of early exercised stock options — ​ — ​ — ​ — ​ 1,921 ​ — ​ — ​ 1,921 Vesting of restricted shares of common stock — ​ — ​ — ​ — ​ 23 ​ — ​ — ​ 23 Repurchase of unvested early exercised stock options — ​ — ​ ( 14,797 ) ​ — ​ — ​ — ​ — ​ — Stock-based compensation expense — ​ — ​ — ​ — ​ 8,625 ​ — ​ — ​ 8,625 Other comprehensive loss, net — ​ — ​ — ​ — ​ — ​ 129 ​ — ​ 129 Net loss — ​ — ​ — ​ — ​ — ​ — ​ ( 154,993 ) ​ ( 154,993 ) 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, 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 ​ The accompanying notes are an integral part of these consolidated financial statements. ​ 125 Table of Contents ALUMIS INC. CONSOLIDATED STATEMENTS OF CASH FLOWS ​ ​ ​ ​ ​ ​ ​ ​ ​ Year ended December 31, (in thousands, except share amounts) ​ 2024 2023 Cash flows from operating activities ​ ​ Net loss ​ $ ( 294,233 ) ​ $ ( 154,993 ) Adjustments to reconcile net loss to net cash used in operating activities: ​ ​ ​ ​ Stock-based compensation ​ 19,457 ​ 8,625 Change in fair value of derivative liability ​ 5,406 ​ 119 Net accretion of discounts on marketable securities ​ ( 3,685 ) ​ ( 544 ) Depreciation and amortization ​ 3,152 ​ 1,284 Non-cash lease expense ​ 60 ​ 2,010 Loss on disposal of fixed assets ​ 5 ​ 266 Write-off of deferred offering costs ​ — ​ 555 Loss on abandonment of right-of-use assets ​ — ​ 645 Changes in operating assets and liabilities: ​ ​ ​ ​ Research and development prepaid expenses ​ ( 10,763 ) ​ 5,526 Other prepaid expenses and other assets ​ ( 2,870 ) ​ ( 340 ) Accounts payable ​ 8,506 ​ ( 642 ) Research and development accrued expenses ​ 18,203 ​ 5,168 Other accrued expenses and current liabilities ​ 3,542 ​ 2,490 Operating lease liabilities ​ ( 1,858 ) ​ ( 144 ) Net cash used in operating activities ​ ( 255,078 ) ​ ( 129,975 ) Cash flows from investing activities ​ ​ Maturities of marketable securities ​ 128,000 ​ 76,250 Purchases of marketable securities ​ ( 240,058 ) ​ ( 11,279 ) Purchases of property and equipment ​ ( 1,732 ) ​ ( 4,499 ) Net cash (used in) provided by investing activities ​ ( 113,790 ) ​ 60,472 Cash flows from financing activities ​ ​ Proceeds from issuance of redeemable convertible preferred stock and derivative liability, net of offering costs ​ 258,461 ​ 89,778 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 ​ 596 ​ 453 Payments of deferred offering costs ​ — ​ ( 485 ) Repurchase of unvested common stock shares issued upon early exercised stock options ​ ( 6 ) ​ ( 64 ) Net cash provided by financing activities ​ 492,367 ​ 89,682 Net increase in cash, cash equivalents and restricted cash ​ 123,499 ​ 20,179 Cash, cash equivalents and restricted cash at beginning of period ​ 47,133 ​ 26,954 Cash, cash equivalents and restricted cash at end of period ​ $ 170,632 ​ $ 47,133 Supplemental disclosures: ​ ​ Conversion of 168,489,871 shares of redeemable convertible preferred stock upon the closing of initial public offering ​ $ 639,237 ​ $ — Settlement of derivative liability upon issuance of redeemable convertible preferred stock ​ $ ( 14,319 ) ​ $ ( 2,231 ) Recognition of derivative liability upon issuance of redeemable convertible preferred stock ​ $ 8,913 ​ $ 2,112 Vesting of early exercised stock options and unvested restricted shares of common stock ​ $ 1,174 ​ $ 1,944 Right-of-use assets obtained in exchange for operating lease liabilities ​ $ — ​ $ 14,255 Property and equipment acquired through tenant improvement allowance ​ $ — ​ $ 16,691 Purchases of property and equipment in other accrued expenses and current liabilities ​ $ — ​ $ 49 Reconciliation of cash, cash equivalents and restricted cash: ​ ​ ​ Cash and cash equivalents ​ $ 169,526 ​ $ 45,996 Restricted cash ​ — ​ 113 Restricted cash, non-current ​ 1,106 ​ 1,024 Total cash, cash equivalents and restricted cash ​ $ 170,632 ​ $ 47,133 ​ The accompanying notes are an integral part of these consolidated financial statements. ​ ​ 126 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, 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 years ended December 31, 2024 and 2023. 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 audited consolidated financial statements have been retrospectively adjusted to reflect the effect of the Reverse Stock Split for all periods presented. The shares of common stock underlying outstanding stock options and other equity instruments were proportionately reduced and the respective exercise prices, if applicable, were proportionately increased in accordance with the terms of the agreements governing such securities. In addition, the conversion ratios for each series of the Company’s redeemable convertible preferred stock, which were automatically convertible into shares of common stock upon the closing of the Company’s initial public offering (“IPO”) of common stock, were proportionally adjusted. IPO and Concurrent Private Placement On June 27, 2024, the Company’s Registration Statement on Form S-1 for its IPO was declared effective, and on July 1, 2024, the Company completed its IPO, pursuant to which it issued and sold 13,125,000 shares of its common stock at $ 16.00 price per share to the public. Net proceeds from the IPO were $ 193.3 million, after deducting underwriting discounts and commissions and other offering costs totaling $ 16.7 million. In connection with the IPO, an existing investor and a holder of more than 5 % of the Company’s capital stock, purchased an additional 2,500,000 shares of the Company’s common stock at the IPO price per share for total gross and net proceeds of $ 40.0 million in a private placement transaction (the “Concurrent Private Placement”). The closing of the Concurrent Private Placement was contingent on the closing of the IPO. The sale of such shares is not registered under the Securities Act of 1933, as amended (the “Securities Act”), and as such, the shares may not be offered or sold absent registration or an applicable exemption from registration. The shares sold in connection with the Concurrent Private Placement are subject to existing resale registration rights and were subject to a 180-day lock-up agreement with the underwriters in the IPO that expired on December 24, 2024. The Concurrent Private Placement closed on July 17, 2024. Immediately prior to the closing of the IPO on July 1, 2024, all of the shares of the Company’s redeemable convertible preferred stock then outstanding converted into 28,855,656 shares of Class A common stock and 7,184,908 shares of Class B common stock at a 1 -for-4.675 conversion ratio (the “Preferred Stock Conversion”). All outstanding Class A common stock shares and all outstanding Class B common stock shares were redesignated immediately thereafter into the same 127 Table of Contents ALUMIS INC. NOTES TO CONSOLIDATED FINANCIAL STATEMENTS number of shares of voting common stock and non-voting common stock, respectively (the “Common Stock Reclassification”). In connection with the closing of the Company’s IPO, the Company increased the authorized number of shares to 500,000,000 shares of common stock and 50,000,000 shares of preferred stock. The authorized number of common stock shares includes voting common stock of 492,815,092 shares and non-voting common stock of 7,184,908 shares. Unless the context otherwise requires a different meaning, all references to “common stock” in these notes refers to the Company’s voting common stock and non-voting common stock combined. Liquidity and Going Concern The Company has incurred negative operating cash flows and significant losses from operations since its inception. For the years ended December 31, 2024 and 2023, the Company incurred net losses of $ 294.2 million and $ 155.0 million, respectively. Cash used in operating activities was $ 255.1 million and $ 130.0 million for the years ended December 31, 2024 and 2023, respectively. As of December 31, 2024, the Company had an accumulated deficit of $ 658.6 million. The Company has historically financed its operations primarily through issuance of common stock, redeemable convertible preferred stock and convertible promissory notes in private placements, and most recently, through its IPO and Concurrent Private Placement. The Company expects to continue to incur substantial losses for the foreseeable future, and its ability to achieve and sustain profitability will depend on the successful development, approval, and commercialization of any product candidates it may develop, and on the achievement of sufficient revenue to support its cost structure. The Company may never achieve profitability and, unless and until it does, it will need to continue to raise additional capital. The Company believes that, based on its current operating plan, its existing cash, cash equivalents and marketable securities of $ 288.3 million as of December 31, 2024, will not be sufficient to meet its operating and capital requirements for at least 12 months from the date of issuance of these consolidated financial statements and there is substantial doubt about the Company’s ability to continue as a going concern. In February 2025, the Company entered into a Merger Agreement (as defined in Note 15) through an all-stock transaction that would improve the Company’s liquidity. However, as of the date of the issuance of these consolidated financial statements, the Merger has not been completed and there can be no assurance that it will be consummated. The Company will need to raise significant additional capital to fund ongoing research and development activities and maintain future operations. The Company’s management plans to monitor expenses and may raise additional capital through a combination of public and private equity, debt financings, strategic alliances, and licensing arrangements. The Company’s ability to access capital when needed is not assured and, if capital is not available to the Company when, and in the amounts, needed, on the terms which are favorable, the Company could be required to delay, scale back, or abandon some or all of its planned development programs and other operations, which could materially harm the Company’s business, financial condition and results of operations. ​ The accompanying consolidated financial statements have been prepared assuming that the Company will continue as a going concern, which contemplates the realization of assets and satisfaction of liabilities in the normal course of business. The accompanying consolidated financial statements do not reflect any adjustments relating to the recoverability and reclassifications of assets and liabilities that might be necessary if the Company is unable to continue as a going concern. ​ 128 Table of Contents ALUMIS INC. NOTES TO CONSOLIDATED FINANCIAL STATEMENTS 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 accounting principles generally accepted in the United States of America (“U.S. GAAP”). Prior to their dissolution, the Company’s consolidated financial statements included the accounts of FronThera U.S. Holdings Inc. and FronThera U.S. Pharmaceuticals LLC, two wholly owned subsidiaries, and all intercompany transactions were eliminated. Any reference in these notes to applicable guidance is meant to refer to the authoritative U.S. GAAP as found in the Accounting Standards Codification (“ASC”) and Accounting Standards Updates (“ASU”) of the Financial Accounting Standards Board (“FASB”). Use of Estimates The preparation of financial statements in conformity with U.S. GAAP requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities, the disclosure of contingent assets and liabilities at the date of the financial statements and the reported amounts of expenses during the reporting period. On an ongoing basis, the Company evaluates estimates and assumptions, including but not limited to those related to accruals for research and development expenses and accruals, stock-based compensation expense, the fair value of common stock and the fair value of the derivative liability. 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 14). 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 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. The Company may also invest in money market funds, U.S. treasuries, commercial paper, corporate bonds, supranational debt securities and agency bonds, which can be subject to certain credit risks. The Company mitigates the risks by investing in high-grade instruments, limiting its exposure to any one issuer and monitoring the ongoing creditworthiness of the financial institutions and issuers. The Company has not experienced any loss of principal on its financial instruments. Risks and Uncertainties The Company is subject to certain risks and uncertainties, including, but not limited to, changes in any of the following areas that the Company believes could have a material adverse effect on the future financial position or results of operations: the Company’s ability to advance the development of its proprietary precision data analytics platform, timing and ability to advance its product candidates through preclinical and clinical development; costs and timelines associated 129 Table of Contents ALUMIS INC. NOTES TO CONSOLIDATED FINANCIAL STATEMENTS 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 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 ongoing conflicts in Ukraine and Israel and the surrounding areas). These worldwide economic conditions may continue into 2025 and may negatively impact the Company’s business, financial position and results of operations. 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 7). Marketable Securities Marketable securities may consist of money market funds, U.S. treasuries, commercial paper, corporate bonds, supranational debt securities and agency bonds 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 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. 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 130 Table of Contents ALUMIS INC. NOTES TO CONSOLIDATED FINANCIAL STATEMENTS instruments, such as money market funds, marketable securities and derivative liabilities are measured at fair value at each reporting date (see Note 3). 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, 2024 and 2023, the Company had no deferred offering costs 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 In-Process Research and Development Expenses The Company measures and recognizes asset acquisitions that are not deemed to be business combinations based on the 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. 131 Table of Contents ALUMIS INC. NOTES TO CONSOLIDATED FINANCIAL STATEMENTS 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, 2024 and 2023, the Company had no finance leases. Impairment of Long-Lived Assets The Company regularly reviews the carrying value and estimated lives of all of its long-lived assets, including property and equipment, and ROU assets to determine whether indicators of impairment may exist which 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, which 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 requires bifurcation, accounts for these at fair value at the issuance date. In May 2024, the Company issued Series C redeemable convertible preferred stock shares, which included embedded derivatives that required bifurcation (see Note 3). 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. 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 (see Note 8). 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 132 Table of Contents ALUMIS INC. NOTES TO CONSOLIDATED FINANCIAL STATEMENTS 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. 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 The Company grants stock-based awards to employees, directors and non-employee consultants in the form of stock options 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. The Company accounts for award forfeitures as they occur. The Company 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. 133 Table of Contents ALUMIS INC. NOTES TO CONSOLIDATED FINANCIAL STATEMENTS 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. Tax benefits related to uncertain tax positions are recognized when it is more likely than not that a tax position will be sustained during an audit. Tax positions that meet the more-likely-than-not threshold are measured at the largest amount of tax benefit that is greater than 50% likely of being realized upon settlement with the taxing authority. Interest and penalties related to unrecognized tax benefits are included within the provision for income tax. 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, 2024 and 2023 consisted of unrealized gain (loss) on marketable securities, net of taxes. 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 common stock issued and outstanding, unvested restricted common stock, early exercised stock options, and redeemable convertible preferred stock issued and outstanding. 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 Jumpstart Our Business Startups Act of 2012, as amended (the “JOBS Act”), and has elected not to “opt out” of the extended transition related to complying with new or revised accounting standards, which means that when a standard is issued or revised and it has different application dates for public and 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 134 Table of Contents ALUMIS INC. NOTES TO CONSOLIDATED FINANCIAL STATEMENTS 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 November 2023, the FASB issued ASU 2023-07, Segment Reporting (Topic 280): Improvements to Reportable Segment Disclosure s (“ASU 2023-07”). This ASU requires public entities to disclose information about their reportable segments’ significant expenses and other segment items on an interim and annual basis. Public entities with a single reportable segment are required to apply the disclosure requirements in ASU 2023-07, as well as all existing segment disclosures and reconciliation requirements in ASC 280 on an interim and annual basis. ASU 2023-07 is effective for fiscal years beginning after December 15, 2023, and for interim periods within fiscal years beginning after December 15, 2024, with early adoption permitted. The Company adopted this standard in the consolidated financial statements for the year ended December 31, 2024. The adoption of this standard did not impact the Company’s reportable segments and additional required disclosures have been included in Note 14. In March 2024, the FASB issued ASU No. 2024-02, Codification Improvements - Amendments to Remove References to the Concepts Statements (“ASU 2024-02”). ASU 2024-02 clarifies and simplifies references to certain concept statements within U.S. GAAP and applies to all reporting entities within the scope of the affected accounting guidance, but in most instances the references removed are extraneous and not required to understand or apply the guidance. ASU 2024-02 is effective for fiscal years 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. The Company adopted this standard in the consolidated financial statements for the year ended December 31, 2024. The adoption of this standard did not have a material impact on its consolidated financial statements at the adoption date. Recently Issued and Not Yet 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 is currently evaluating the impact of this standard on its disclosure in its consolidated financial statements. 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 Company is currently evaluating the impact of adopting ASU 2024-03 on its consolidated financial statements and disclosures. 3. Fair Value Measurements The Company discloses and recognizes the fair value of its assets and liabilities using a hierarchy that prioritizes the inputs to valuation techniques used to measure fair value. The guidance establishes three levels of the fair value hierarchy as follows: Level 1—Quoted prices in active markets for identical assets or liabilities. Level 2—Observable inputs other than Level 1 prices, such as quoted prices for similar assets or liabilities, quoted prices in markets that are not active, or other inputs that are observable or can be corroborated by observable market data for 135 Table of Contents ALUMIS INC. NOTES TO CONSOLIDATED FINANCIAL STATEMENTS substantially the full term of the assets or liabilities. Level 3—Unobservable inputs that are supported by little or no market activity and that are significant to the fair value of the assets or liabilities. Assets and liabilities measured at fair value are classified in their entirety based on the lowest level of input that is significant to the fair value measurement. The Company’s assessment of the significance of a particular input to the fair value measurement in its entirety requires management to make judgments and consider factors specific to the asset or liability. The Company recognizes transfers into and out of levels within the fair value hierarchy in the period in which the actual event or change in circumstances that caused the transfer occurs. The Company’s financial instruments consist of Level 1, Level 2 and Level 3 financial instruments. Changes in the ability to observe valuation inputs may result in a reclassification of levels of certain securities within the fair value hierarchy. Level 1 financial instruments are comprised of money market funds and U.S. treasuries. Level 2 financial instruments are comprised of U.S. treasuries. Usually, short term marketable securities are considered Level 2 when their fair values are determined using inputs that are observable in the market or can be derived principally from or corroborated by observable market data such as pricing for similar securities, recently executed transactions, cash flow models with yield curves, and benchmark securities. In addition, Level 2 financial instruments are valued using comparisons to like-kind financial instruments and models that use readily observable market data as their basis. Level 3 financial instruments include derivative liabilities issued in May 2023 and settled in October 2023 in connection with the closing of the second tranche of the Series B-2 and B-2A redeemable convertible preferred stock financing, and issued in March 2024 and settled in May 2024 in connection with the closing of the second tranche of the Series C redeemable convertible preferred stock financing. The following tables represent the Company’s fair value hierarchy for financial assets measured at fair value on a recurring basis as of December 31, 2024 and 2023 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Fair Value Measurements as of December 31, 2024 ​ Level 1 Level 2 Level 3 Total Assets: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Cash equivalents ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Money market funds ​ $ 168,847 ​ $ — ​ $ — ​ $ 168,847 Marketable securities ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ U.S. treasuries ​ 47,137 ​ 71,600 ​ — ​ 118,737 Total assets ​ $ 215,984 ​ $ 71,600 ​ $ — ​ $ 287,584 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Fair Value Measurements as of December 31, 2023 ​ Level 1 Level 2 Level 3 Total Assets: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Cash equivalents ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Money market funds ​ $ 21,310 ​ $ — ​ $ — ​ $ 21,310 U.S. treasuries ​ ​ 2,000 ​ ​ — ​ ​ — ​ ​ 2,000 Marketable securities ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ U.S. treasuries ​ 1,958 ​ 998 ​ — ​ 2,956 Total assets ​ $ 25,268 ​ $ 998 ​ $ — ​ $ 26,266 ​ ​ The derivative liability issued in May 2023 in connection with the closing of the second tranche of the Series B-2 and B-2A redeemable convertible preferred stock financing was a freestanding financial instrument and represented the Company’s obligation to issue additional shares of Series B-2 and B-2A redeemable convertible preferred stock at a fixed price upon the approval by the Company’s board of directors. In connection with the Series C redeemable convertible preferred stock financing in March 2024, the Company issued to investors two freestanding financial instruments: the 136 Table of Contents ALUMIS INC. NOTES TO CONSOLIDATED FINANCIAL STATEMENTS 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. ​ ​ The following table provides a range of assumptions used in the valuation of the derivative liability for the years ended December 31, 2024 and 2023: ​ ​ ​ ​ ​ ​ ​ ​ ​ Year Ended December 31, ​ ​ 2024 2023 Expected term (in years) ​ 0.2 – 0.4 ​ ​ 0.0 – 0.4 ​ Volatility 55.1 % – 59.9 % ​ 43.2 % – 83.2 % Risk-free interest rate 5.4 % – 5.5 % % ​ 5.2 % – 5.6 % Dividend yield 0.0 % ​ 0.0 % Probability of option exercise 0.0 % – 100.0 % % ​ 30.0 % – 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 years ended December 31, 2024 and 2023 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ Year Ended December 31, ​ ​ 2024 2023 Fair value at beginning of period ​ $ — ​ $ — Fair value upon issuance ​ 8,913 ​ ​ 2,112 Changes in fair value ​ 5,406 ​ ​ 119 Fair value upon settlement ​ ( 14,319 ) ​ ​ ( 2,231 ) Fair value at end of period $ — ​ $ — ​ There were no transfers between Level 1, Level 2 or Level 3 categories for the years ended December 31, 2024 and 2023. 4. Marketable Securities Marketable securities, which are classified as available-for-sale, consisted of the following as of December 31, 2024 and 2023 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Gross Gross Fair Value as of ​ ​ Amortized Cost ​ Unrealized ​ Unrealized ​ December 31, ​ ​ Basis ​ Gains ​ Losses ​ 2024 Short-term marketable securities: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ U.S. treasuries ​ $ 118,697 ​ $ 45 ​ $ ( 5 ) ​ $ 118,737 Total short-term marketable securities ​ $ 118,697 ​ $ 45 ​ $ ( 5 ) ​ $ 118,737 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Gross Gross Fair Value as of ​ ​ Amortized Cost ​ Unrealized ​ Unrealized ​ December 31, ​ ​ Basis ​ Gains ​ Losses ​ 2023 Short-term marketable securities: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ U.S. treasuries ​ $ 2,954 ​ $ 2 ​ $ — $ 2,956 Total short-term marketable securities ​ $ 2,954 ​ $ 2 ​ $ — $ 2,956 ​ ​ All marketable securities held as of December 31, 2024 and 2023 had contractual maturities of less than one year. 137 Table of Contents ALUMIS INC. NOTES TO CONSOLIDATED FINANCIAL STATEMENTS As of December 31, 2024 and 2023, no significant facts or circumstances were present to indicate a deterioration in the creditworthiness of the issuers of the marketable securities, and the Company has no requirement or intention to sell these securities before maturity or recovery of their amortized cost basis. The Company considered the current and expected future economic and market conditions and determined that its 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, 2024 and 2023, the Company did no t recognize any impairment losses on its marketable securities. 5. Balance Sheet Components Other Prepaid Expenses and Current Assets Other prepaid expenses and current assets consisted of the following as of December 31, 2024 and 2023 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ December 31, December 31, ​ ​ 2024 ​ 2023 Prepaid insurance ​ $ 695 ​ $ 111 Prepaid subscriptions ​ ​ 1,232 ​ ​ 703 Interest receivable ​ ​ 698 ​ ​ 108 Tax receivable ​ ​ 1,114 ​ ​ 614 Other ​ 762 ​ 95 Total other prepaid expenses and current assets ​ $ 4,501 ​ $ 1,631 ​ Property and Equipment, net Property and equipment, net consisted of the following as of December 31, 2024 and 2023 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Estimated Useful Life December 31, December 31, ​ ​ (in years) ​ 2024 ​ 2023 Leasehold improvements Shorter of useful life or lease term ​ $ 17,618 ​ $ 17,592 Laboratory equipment 5 ​ ​ 5,227 ​ ​ 3,577 Furniture and fixtures 5 ​ 1,709 ​ 1,709 Computer equipment 5 ​ 896 ​ 896 Capitalized software 3 ​ 75 ​ 75 Total property and equipment, gross ​ ​ ​ 25,525 ​ 23,849 Less: Accumulated depreciation and amortization ​ ​ ​ ( 4,557 ) ​ ( 1,408 ) Total property and equipment, net ​ ​ ​ $ 20,968 ​ $ 22,441 ​ Depreciation and amortization expense was $ 3.2 million and $ 1.3 million for the years ended December 31, 2024 and 2023, respectively. 138 Table of Contents ALUMIS INC. NOTES TO CONSOLIDATED FINANCIAL STATEMENTS Other Accrued Expenses and Current Liabilities Other accrued expenses and current liabilities consisted of the following as of December 31, 2024 and 2023 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ December 31, December 31, ​ ​ 2024 ​ 2023 Accrued personnel and related expenses ​ $ 7,765 ​ $ 5,585 Accrued professional services ​ 2,657 ​ 1,093 Accrued other expenses ​ 158 ​ 409 Total other accrued expenses and current liabilities ​ $ 10,580 ​ $ 7,087 ​ 6. 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, 2024 and 2023, the Company recognized $ 0.9 million and $ 1.5 million as research and development expenses under the service agreement, respectively. Accrued expenses under the service agreement were zero and $ 2 thousand as of December 31, 2024 and 2023, respectively. 7. Commitments and Contingent Liabilities Operating Leases In 2021, the Company entered into a lease agreement for 14,000 square feet of office space in South San Francisco, California, which commenced in August 2021 and had a contractual termination date of September 2024. In September 2023, the Company abandoned this right-of-use asset as it had moved to its new office space described below; the Company recognized a loss on this abandonment in the amount of $ 0.6 million. In January 2022, the Company entered into a lease agreement for 12,000 square feet of office and laboratory space in South San Francisco, California, which commenced in July 2022 and had a contractual termination date of July 2029. This lease contained an early termination option, allowing the Company to terminate this lease before the expiry of the lease term. The Company concluded the lease term for accounting purposes ended in August 2023. In April 2023, the lease was modified, and the contractual lease termination was changed to October 2023. The accounting impact of the modification was not material. 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 Company constructed leasehold improvements in the space, which were concluded to be lessee assets. The lessor provided the Company a tenant improvement allowance of $ 17.2 million, of which $ 0.5 million and $ 16.7 million were received and were accounted for as a reduction to lease payments for the years ended December 31, 2022 and 2023, respectively. At the commencement date, future lease payments totaled $ 37.9 million, including $ 54.6 million in gross fixed payments less $ 16.7 million in lease incentives received during the first year of the lease. The lease liability at lease commencement was calculated to be $ 14.1 million, which is equal to the present value of the future lease payments, discounted at the incremental borrowing rate of 11.4 %. Following the commencement date, the Company measured its lease liability and right-of-use asset in accordance with ASC 842-20-35-3. In accordance with this guidance, future lease payments increased as the $ 16.7 million incentive was received, and future gross fixed payments were no longer offset by these incentives. Leasehold improvements were reflected in property and equipment, net in the consolidated balance sheets as of 139 Table of Contents ALUMIS INC. NOTES TO CONSOLIDATED FINANCIAL STATEMENTS December 31, 2024 and 2023. The lease agreement also 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 not reasonably certain that the lease will be extended. Therefore, the Company will recognize the right-of-use asset and the lease liability on the commencement date in January 2025. Total undiscounted lease payments over the lease term will be approximately $ 1.9 million. The Company maintains letters of credit representing security deposits on its leases in the amount of $ 1.1 million as of December 31, 2024 and 2023. The letters of credit were reflected in restricted cash, non-current in the consolidated balance sheets as of December 31, 2024 and in restricted cash, current and non-current in the consolidated balance sheets as of December 31, 2023. The components of lease costs were as follows (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ Year Ended December 31, ​ ​ 2024 ​ 2023 Operating lease costs ​ $ 3,469 ​ $ 4,747 Variable lease costs ​ 1,202 ​ 545 Total lease costs ​ $ 4,671 ​ $ 5,292 ​ Supplemental cash flow information related to the operating leases were as follows (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ Year Ended December 31, ​ ​ 2024 ​ 2023 Cash payments included in the measurement of operating lease liabilities ​ $ 5,299 ​ $ 2,903 ​ Weighted-average remaining lease term and incremental borrowing rate for the operating leases were as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, ​ December 31, ​ ​ 2024 2023 ​ Weighted-average remaining lease term (years) 8.7 ​ 9.5 ​ Weighted-average incremental borrowing rate 11.4 % 11.4 % ​ Future minimum lease payments under non-cancelable leases as of December 31, 2024 were as detailed below (in thousands): ​ ​ ​ ​ 2025 ​ $ 4,959 2026 ​ ​ 5,125 2027 ​ 5,296 2028 ​ 5,474 2029 ​ 5,658 Thereafter ​ 21,857 Total undiscounted lease payments ​ 48,369 Less: Imputed interest ​ ( 17,647 ) Total operating lease liabilities ​ $ 30,722 ​ 140 Table of Contents ALUMIS INC. NOTES TO CONSOLIDATED FINANCIAL STATEMENTS FronThera Contingent Consideration In March 2021, the Company entered into a stock purchase agreement to acquire FronThera U.S. Holdings, Inc. and its wholly owned subsidiary, FronThera U.S. Pharmaceuticals LLC., 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, 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 ESK-001 to a patient enrolled in a Phase 2 clinical trial of ESK-001, which 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 ESK-001 to a patient enrolled in a Phase 3 clinical trial of ESK-001 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, 2024. Research and Development Agreements The Company enters into various agreements in the ordinary course of business, such as those with suppliers, CROs, CMOs and clinical trial sites. These agreements provide for termination at the request of either party, generally with less than one-year notice and are, therefore, cancellable contracts and, if cancelled, are not anticipated to have a material effect on the Company’s financial condition, results of operations, or cash flows. Legal Contingencies From time to time, the Company may become involved in legal proceedings arising from the ordinary course of business. 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. Management is currently not aware of any legal matters that could have a material adverse effect on the Company’s financial position, results of operations or cash flows. 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, 2024 and 2023, the Company did not have any material indemnification claims that were probable or reasonably possible and consequently has not recorded related liabilities. 8. Redeemable Convertible Preferred Stock In May 2023, the Company issued and sold an aggregate of 10,722,340 shares of Series B-2 redeemable convertible preferred stock for gross proceeds of $ 53.6 million and 1,277,660 shares of Series B-2A redeemable convertible preferred stock for gross proceeds of $ 6.4 million and incurred $ 0.2 million of offering costs. The purchase price for Series B-2 and B-2A redeemable convertible preferred stock was $ 5.00 per share. The Series B-2 and Series B-2A stock purchase agreement contained an obligation to issue additional shares of Series B-2 or Series B-2A redeemable convertible preferred stock in a second tranche closing by October 2023 (the “Second Tranche Series B-2 Closing”) upon the occurrence of certain events, including the board of directors’ consent. The Company recognized this call option as a derivative liability and estimated its fair value of $ 2.1 million. 141 Table of Contents ALUMIS INC. NOTES TO CONSOLIDATED FINANCIAL STATEMENTS In July 2023, the holders of the shares of Series B-2A redeemable convertible preferred stock elected to convert their 1,277,660 shares into the same number of Series B-2 redeemable convertible preferred stock. In October 2023, the Company closed the Second Tranche Series B-2 Closing and issued an additional 4,221,170 shares of Series B-2 redeemable convertible preferred stock and 1,778,830 shares of Series B-2A redeemable convertible preferred stock at a price of $ 5.00 per share and received gross proceeds of $ 21.1 million and $ 8.9 million, respectively. Accordingly, the derivative liability was settled, and the Company reclassified the derivative liability, remeasured at fair value of $ 2.2 million, into redeemable convertible preferred stock. The Company incurred less than $ 0.1 million of offering costs in connection with the Second Tranche Series B-2 Closing. 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 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 (see Note 1) and are no longer outstanding. 142 Table of Contents ALUMIS INC. NOTES TO CONSOLIDATED FINANCIAL STATEMENTS The Company’s redeemable convertible preferred stock as of December 31, 2023, consisted of the following: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, 2023 ​ ​ ​ ​ Shares Issued ​ Aggregate ​ ​ ​ ​ ​ Shares ​ and ​ Liquidation ​ Net Carrying ​ Authorized Outstanding Preference Value ​ ​ (in thousands, except share amounts) Series Seed redeemable convertible preferred stock 10,500,000 10,500,000 ​ $ 10,500 ​ $ 10,480 Series A redeemable convertible preferred stock 7,500,000 7,500,000 ​ 30,000 ​ 29,972 Series B redeemable convertible preferred stock 40,200,000 40,200,000 ​ 201,000 ​ 200,711 Series B-1 redeemable convertible preferred stock 9,760,088 9,760,088 ​ 39,040 ​ 44,310 Series B-2 redeemable convertible preferred stock ​ 18,000,000 ​ 16,221,170 ​ ​ 81,106 ​ ​ 80,969 Series B-2A redeemable convertible preferred stock ​ 3,056,490 ​ 1,778,830 ​ ​ 8,894 ​ ​ 8,928 Total redeemable convertible preferred stock 89,016,578 85,960,088 ​ $ 370,540 ​ $ 375,370 ​ 9. 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 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, 2024, there were no shares of preferred stock issued or outstanding, and 47,222,419 and 7,184,908 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). 143 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, 2024 and 2023: ​ ​ ​ ​ ​ ​ ​ December 31, December 31, ​ ​ 2024 ​ 2023 Outstanding and issued stock options 9,458,788 5,096,086 Shares available for grant under 2024 Equity Incentive Plan ​ 6,893,517 ​ — Shares available for grant under 2024 Employee Stock Purchase Plan ​ 650,000 ​ — Shares available for grant under 2024 Performance Option Plan ​ 92,800 ​ — Shares available for grant under 2021 Stock Plan — 296,189 Redeemable convertible preferred stock issued and outstanding — 18,387,168 Total 17,095,105 23,779,443 ​ 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 vest over a four-year period with a one-year cliff vesting. The holders have voting and dividends rights. The Company has 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 is recognized ratably over the vesting terms. The Company recognized $ 0.1 million of stock-based compensation expense related to restricted stock awards for each of the years ended December 31, 2024 and 2023. In the year ended December 31, 2024, a holder’s continuous service terminated, and the Company repurchased the unvested shares. The following table summarizes the activity for the Company’s restricted common stock for the years ended December 31, 2024 and 2023: ​ ​ ​ ​ ​ ​ ​ ​ ​ Weighted- ​ ​ ​ ​ Average ​ ​ Number of ​ Grant Date ​ ​ Shares ​ Fair Value Unvested as of December 31, 2023 29,322 ​ $ 2.90 Vested ( 20,322 ) ​ $ 2.90 Repurchased ​ ( 6,417 ) ​ $ 2.90 Unvested as of December 31, 2024 2,583 ​ $ 2.90 ​ As of December 31, 2024, the remaining unamortized stock-based compensation expense was immaterial. 10. Stock-Based Compensation 2021 Stock Plan In February 2021, the Company adopted its 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”), restricted stock units (“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. 144 Table of Contents ALUMIS INC. NOTES TO CONSOLIDATED FINANCIAL STATEMENTS 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 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 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. 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 , or increased to $ 1,000,000 in the fiscal year of their initial service as a non- 145 Table of Contents ALUMIS INC. NOTES TO CONSOLIDATED FINANCIAL STATEMENTS employee director. The terms of the 2024 EIP do not permit option holders to exercise options before their options are vested. 2024 Employee Stock Purchase Plan ​ In June 2024, the Company’s board of directors adopted, and its stockholders approved, the 2024 Employee Stock Purchase Plan (the “2024 ESPP”), which became effective on June 28, 2024, upon execution of the underwriting agreement related to the Company’s IPO. The Company 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. 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 board of directors. In December 2024, the Company’s board of directors approved the grant of purchase rights under an offering period beginning on January 24, 2025. Stock Option Activity 2021 Plan and 2024 EIP The following table summarizes the Company’s stock option activity under the 2021 Plan and 2024 EIP for the years ended December 31, 2024 and 2023. The table 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, 2023 5,096,086 ​ $ 9.68 8.5 ​ $ 15,033 Granted 2,902,385 ​ $ 11.68 ​ ​ ​ ​ ​ Exercised ( 72,201 ) ​ $ 8.26 ​ ​ ​ $ 333 Forfeited or expired ( 255,362 ) ​ $ 10.23 ​ ​ ​ ​ ​ Outstanding, vested and expected to vest as of December 31, 2024 7,670,908 ​ $ 9.59 ​ 8.2 ​ $ 1,777 Exercisable as of December 31, 2024 ​ 6,565,317 ​ $ 9.31 ​ 8.0 ​ $ 1,777 ​ Total exercisable shares of 6,565,317 as of December 31, 2024 included 3,906,969 unvested shares that were early exercisable under the 2021 Plan. 146 Table of Contents ALUMIS INC. NOTES TO CONSOLIDATED FINANCIAL STATEMENTS 2024 POP The following table summarizes the Company’s stock option activity under the 2024 POP for the year ended December 31, 2024. ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Weighted- ​ ​ ​ ​ ​ ​ Weighted- ​ Average ​ ​ ​ ​ ​ ​ ​ Average ​ Remaining ​ Aggregate ​ ​ ​ ​ Exercise ​ Contractual ​ Intrinsic ​ ​ ​ ​ Price Per ​ Term ​ Value ​ ​ Options ​ Share ​ (in years) ​ (in thousands) Outstanding as of December 31, 2023 — ​ $ — ​ — ​ $ — Granted 1,880,680 ​ $ 10.19 ​ ​ ​ Forfeited or expired ( 92,800 ) ​ $ 10.19 ​ ​ ​ ​ Outstanding, vested and expected to vest as of December 31, 2024 1,787,880 ​ $ 10.19 ​ 9.3 ​ $ — Exercisable as of December 31, 2024 — ​ $ — ​ — ​ $ — ​ Valuation of Stock Options Granted Under the 2021 Plan and 2024 EIP The weighted-average grant date fair value of stock options granted under the 2021 Plan and the 2024 EIP for the years ended December 31, 2024 and 2023 was $ 9.92 and $ 10.93 per stock option, respectively. The total fair value of stock options vested for the years ended December 31, 2024 and 2023 was $ 5.8 million and $ 8.1 million, respectively. The fair value of these stock options was estimated using the Black-Scholes option pricing model with the following assumptions: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year Ended December 31, ​ 2024 2023 Expected term (in years) ​ 5.8 – 6.1 ​ 5.8 – 6.6 ​ Volatility ​ 103.65 % – 109.78 % ​ 97.65 % – 102.54 % Risk-free interest rate ​ 3.47 % – 4.48 % ​ 3.66 % – 4.77 % 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. 147 Table of Contents ALUMIS INC. NOTES TO CONSOLIDATED FINANCIAL STATEMENTS 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. Common Stock Fair Value Prior to the IPO, the fair market value of the Company’s common stock was determined by the board of directors with assistance from management and external valuation experts. The approach to estimating the fair market value of common stock was consistent with the methods outlined in the Practice Aid. Prior to May 2023, the Company utilized an Option Pricing Method (“OPM”) based analysis, primarily the OPM backsolve methodology, to determine the estimated fair value of the common stock. Within the OPM framework, the backsolve method, for inferring the total equity value implied by a recent financing transaction or by an estimated equity value of the Company’s pipeline product candidates, involves the construction of an allocation model that takes into account the Company’s capital structure and the rights, preferences and privileges of each class of stock, then assumes reasonable inputs for the other OPM variables (expected time to liquidity, volatility, and risk-free rate). The total equity value is then iterated in the model until the model output value for the equity class sold in a recent financing round equals the price paid in that round. The OPM is generally utilized when specific future liquidity events are difficult to forecast (i.e., the enterprise has many choices and options available), and the enterprise’s value depends on how well it follows an uncharted path through the various possible opportunities and challenges. In determining the estimated fair value of the common stock, the board of directors also considered the fact that the stockholders could not freely trade the common stock in the public markets. Accordingly, the Company applied discounts to reflect the lack of marketability of its common stock based on the weighted-average expected time to liquidity. The estimated fair value of the common stock at each grant date reflected a non-marketability discount partially based on the anticipated likelihood and timing of a future liquidity event. For valuations performed between May 2024 and before June 27, 2024, the Company utilized a hybrid method that combined the Probability-Weighted Expected Return Method (“PWERM”), an accepted valuation method described in the Practice Aid, and the OPM. The Company determined this was the most appropriate method for determining the fair value of its common stock based on the stage of development and other relevant factors. The PWERM is a scenario-based analysis that estimates the value per share of common stock based on the probability-weighted present value of expected future equity values for the common stock, under various possible future liquidity event scenarios, considering the rights and preferences of each class of shares, discounted for a lack of marketability. Under the hybrid method, an OPM was utilized to determine the fair value of the Company’s common stock in certain of the PWERM scenarios (capturing situations where its development path and future liquidity events were difficult to forecast), potential exit events were explicitly modeled in the other PWERM scenarios. A discount for lack of marketability was applied to the value derived under each scenario to account for a lack of access to an active public market to estimate the common stock fair value. The Company also considered the amount of time between the independent third-party valuation dates and the grant dates and performed an interpolation of the fair value between the two valuation dates to estimate common stock fair value at each grant date. This determination includes an evaluation of whether the subsequent valuation indicated that any significant change in valuation had occurred between the previous valuation and the grant date. The assumptions underlying these valuations represented management’s best estimates, which involved inherent uncertainties and the application of management’s judgment. As a result, if the Company had used significantly different assumptions or estimates, the fair value of the common stock and the stock-based compensation expense could have been materially different. Once a public trading market for the Company’s common stock was established in connection with its IPO, the fair value of the Company’s common stock was based on the IPO price per share and thereafter on its publicly traded common stock price at grant date, as listed on the Nasdaq Global Select Market under the ticker “ALMS.” 148 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. The Company recognized $ 5.7 million in stock-based compensation expense related to the 2024 POP for the year ended December 31, 2024. 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, 2024 and 2023, there was $ 0.8 million and $ 1.8 million share repurchase liability related to the unvested shares, respectively, included in share repurchase liability in the consolidated balance sheets. The following table summarizes the activity for the Company’s early exercisable shares for the years ended December 31, 2024 and 2023: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Weighted- ​ ​ ​ ​ Average ​ ​ Number of ​ Exercise Price ​ Shares Per Share Unvested as of December 31, 2022 663,930 ​ $ 5.36 Early exercised 18,469 ​ $ 9.48 Vested ( 340,502 ) ​ $ 5.65 Repurchased ( 14,797 ) ​ $ 4.36 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 ​ 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, 2024 and 2023 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ Year Ended December 31, ​ ​ 2024 ​ 2023 Research and development ​ $ 10,110 ​ $ 4,745 General and administrative ​ 9,347 ​ 3,880 Total stock-based compensation expense ​ $ 19,457 ​ $ 8,625 149 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, 2024 and 2023 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ Year Ended December 31, ​ ​ 2024 ​ 2023 Stock options ​ $ 19,399 ​ $ 8,553 Restricted stock awards ​ 58 ​ 72 Total stock-based compensation expense ​ $ 19,457 ​ $ 8,625 ​ Stock-based compensation expense related to non-employee awards was $ 0.3 million for the years ended December 31, 2024 and 2023. As of December 31, 2024, there was unrecognized stock-based compensation expense of $ 54.4 million related to unvested stock options which the Company expects to recognize over a remaining weighted-average period of 2.5 years. 11. Net Loss Per Share Attributable to Common Stockholders The following table sets forth the computation of the basic and diluted net loss per share attributable to common stockholders for the years ended December 31, 2024 and 2023 (in thousands, except share and per share amounts): ​ ​ ​ ​ ​ ​ ​ ​ ​ Year Ended December 31, ​ ​ 2024 ​ 2023 Numerator: ​ ​ ​ ​ ​ ​ Net loss ​ $ ( 294,233 ) ​ $ ( 154,993 ) Denominator: ​ ​ Weighted-average shares of common stock outstanding ​ 28,579,979 ​ 2,649,038 Less: Weighted-average shares of common stock subject to repurchase ​ ( 238,113 ) ​ ( 498,852 ) Weighted-average shares of common stock outstanding, basic and diluted ​ ​ 28,341,866 ​ ​ 2,150,186 Net loss per share attributable to common stockholders, basic and diluted ​ $ ( 10.38 ) ​ $ ( 72.08 ) ​ 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, 2024 December 31, 2023 Stock options issued and outstanding 9,458,788 5,096,086 Unvested restricted common stock and early exercised stock options 149,266 356,422 Redeemable convertible preferred stock issued and outstanding ​ — ​ 18,387,168 Total 9,608,054 23,839,676 ​ ​ ​ 12. Income Taxes No provision for income taxes was recorded for the years ended December 31, 2024 and 2023, as the Company operated with taxable losses. The Company has incurred net operating losses only in the United States since inception. 150 Table of Contents ALUMIS INC. NOTES TO CONSOLIDATED FINANCIAL STATEMENTS The differences between the effective income tax rate and the U.S. federal statutory income tax rate for the years ended December 31, 2024 and 2023 were as follows (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ Year Ended December 31, ​ ​ 2024 ​ 2023 Amount at statutory tax rates ​ $ ( 61,789 ) ​ $ ( 32,548 ) Permanent differences ​ 3,000 ​ 7 Valuation allowance ​ 64,923 ​ 34,961 Stock-based compensation ​ 3,356 ​ 892 Federal research and development credit ​ ( 9,520 ) ​ ( 3,322 ) Other ​ 30 ​ 10 Total ​ $ — ​ $ — ​ Significant components of the deferred tax asset balances as of December 31, 2024 and 2023 were as follows (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ December 31, December 31, ​ ​ 2024 ​ 2023 Deferred tax assets: ​ ​ ​ ​ ​ ​ Net operating losses ​ $ 21,573 ​ $ 10,519 Tax credits ​ 17,407 ​ 6,243 Research and development capitalization ​ 74,211 ​ 39,059 Accruals and reserves ​ 115 ​ 15 Stock-based compensation ​ 3,088 ​ 1,361 Operating lease liabilities ​ 6,452 ​ 6,842 Other capitalized expenses ​ 11,832 ​ 4,567 Gross deferred tax assets ​ 134,678 ​ 68,606 Valuation allowance ​ ( 127,990 ) ​ ( 61,404 ) Deferred tax assets, net of valuation allowance ​ $ 6,688 ​ $ 7,202 Deferred tax liabilities: ​ ​ ​ ​ ​ ​ Fixed assets ​ ( 885 ) ​ ( 1,025 ) Operating lease right-of-use assets ​ ( 5,803 ) ​ ( 6,177 ) Deferred tax liabilities ​ ( 6,688 ) ​ ( 7,202 ) Total net deferred tax assets ​ $ — ​ $ — ​ 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 full valuation allowance has been recorded. The valuation allowance increased by $ 66.6 million and by $ 35.4 million for the years ended December 31, 2024 and 2023, respectively, primarily due to the net operating losses carryforwards and research and development credits. The following table sets forth the Company’s U.S. federal and state net operating loss carryforwards and tax credits as of December 31, 2024 (in thousands): ​ ​ ​ ​ ​ ​ ​ Amount Begin to Expire Net operating losses, U.S. federal ​ $ 84,664 Do not expire Net operating losses, U.S. federal ​ $ 16,520 2037 Net operating losses, U.S. states ​ $ 4,683 2041 Tax credits, U.S. federal ​ $ 16,026 2039 Tax credits, U.S. states ​ $ 5,289 2037 ​ 151 Table of Contents ALUMIS INC. NOTES TO CONSOLIDATED FINANCIAL STATEMENTS 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, 2024, the Company has completed an Internal Revenue Code section 382 analysis which did not result in any expiration of U.S. federal net operating losses and credits before utilization. As the Company has recorded a full valuation allowance, any potential limitation is not expected to have a material impact to the 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, 2024 and 2023, is as follows (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ Year Ended December 31, ​ ​ 2024 ​ 2023 Beginning balance ​ $ 4,116 ​ $ 2,451 Increases in tax positions in the current period ​ 1,336 ​ 3,572 Decreases related to prior year’s tax position ​ ( 2,655 ) ​ ( 1,907 ) Ending balance ​ $ 2,797 ​ $ 4,116 ​ 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, 2024 and 2023, the Company did no t recognize accrued interest and penalties related to unrecognized tax benefits. The Company does no t anticipate that the amount of existing unrecognized tax benefits will significantly increase or decrease during the next 12 months. As of December 31, 2024, 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. 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, 2024 and 2023. 14. 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. 152 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, 2024 and 2023 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ Year Ended December 31, ​ 2024 2023 Operating expenses: ​ ​ ​ ​ ​ ​ Research and development expenses ​ ​ ​ ​ ​ ​ External costs ​ ​ ​ ​ ​ ​ Milestones related to previously acquired IPR&D assets ​ $ 23,000 ​ $ — CRO, CMO and clinical trials ​ ​ 151,422 ​ ​ 68,967 Professional consulting services ​ ​ 19,154 ​ ​ 13,155 Other research and development costs ​ ​ 10,258 ​ ​ 11,463 Internal costs ​ ​ ​ ​ ​ ​ Personnel-related costs ​ ​ 46,774 ​ ​ 32,068 Facilities and overhead costs ​ ​ 14,946 ​ ​ 12,023 Total research and development expense ​ ​ 265,554 ​ ​ 137,676 General and administrative expenses ​ ​ 35,200 ​ ​ 20,498 Total operating expenses ​ 300,754 ​ 158,174 Loss from operations ​ ( 300,754 ) ​ ( 158,174 ) Total other income (expense), net ​ 6,521 ​ 3,181 Consolidated net loss ​ $ ( 294,233 ) ​ $ ( 154,993 ) ​ ​ ​ 15. Subsequent Events Merger Agreement On February 6, 2025, the Company entered into an Agreement and Plan of Merger (the “Merger Agreement”) with ACELYRIN, Inc., a Delaware corporation (“ACELYRIN”), and Arrow Merger Sub, Inc., a Delaware corporation and a direct wholly owned subsidiary of the Company (“Merger Sub”). Under the terms of the Merger Agreement, Merger Sub will merge with and into ACELYRIN, with ACELYRIN continuing as a direct wholly owned subsidiary of the Company (the “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 is subject to stockholder approval by the stockholders of each company and satisfaction or waiver of other closing conditions. In connection with the Merger, all of the issued and outstanding shares of common stock of ACELYRIN, par value $ 0.00001 per share (the “ACELYRIN Shares”), will be cancelled and converted into the right to receive 0.4274 shares of the Company’s voting common stock, without interest (the number of shares of the Company’s common stock in exchange for each ACELYRIN Share, the “Exchange Ratio”) and, if applicable, cash in lieu of fractional shares, subject to any applicable withholding. ​ Consummation of the Merger is subject to certain closing conditions, including the absence of any law or judgment that restrains, enjoins or otherwise prohibits consummation of the Merger, the effectiveness of a registration statement on Form S-4 to be filed with the SEC by the Company, adoption of the Merger Agreement by the holders of a majority of the outstanding ACELYRIN Shares at ACELYRIN’s stockholders’ meeting, and approval of the share issuance by the holders of a majority of votes of the Company’s common stock cast at the Company’s stockholders’ meeting. The Merger Agreement contains certain termination rights for both the Company and ACELYRIN, including the right of either party to terminate the Merger Agreement if the transactions have not been consummated prior to July 7, 2025. The Company or ACELYRIN will pay a termination fee of $ 10.0 million or $ 10.0 million, respectively, under certain circumstances, including termination to accept and enter into a definitive agreement with respect to a superior proposal. 153 Table of Contents ALUMIS INC. NOTES TO CONSOLIDATED FINANCIAL STATEMENTS Immediately following the Merger, the Company’s pre-Merger equityholders are expected to collectively own approximately 55 % of the shares of the combined company and the pre-Merger equityholders of ACELYRIN as of immediately prior to the Merger are expected to collectively own approximately 45 % of the combined company, in each case, calculated on a fully diluted basis as of January 31, 2025. ​ ​ 154 Table of Contents Item 9. Changes in and Disagreements with Accountants on Accounting and Financial Disclosure None.