ALUMIS INC. 10-Q

Item 1. Financial Statements (Unaudited) ALUMIS INC. CONDENSED CONSOLIDATED BALANCE SHEETS ​ (Unaudited) ​ ​ ​ ​ ​ ​ ​ ​ ​ June 30, December 31, (in thousands, except share and per share amounts) ​ 2024 ​ 2023 Assets ​ ​ Current assets ​ ​ Cash and cash equivalents ​ $ 155,108 ​ $ 45,996 Restricted cash ​ 113 ​ 113 Marketable securities ​ 54,423 ​ 2,956 Research and development prepaid expenses ​ 13,200 ​ 2,661 Other prepaid expenses and current assets ​ 2,012 ​ 1,631 Total current assets ​ 224,856 ​ 53,357 Restricted cash, non-current ​ 1,024 ​ 1,024 Property and equipment, net ​ 22,173 ​ 22,441 Operating lease right-of-use assets, net ​ 12,772 ​ 12,783 Other long-term assets ​ 4,354 ​ 7 Total assets ​ $ 265,179 ​ $ 89,612 Liabilities, Redeemable Convertible Preferred Stock and Stockholders’ Deficit ​ ​ Current liabilities ​ ​ Accounts payable ​ $ 9,188 ​ $ 1,118 Research and development accrued expenses ​ 14,584 ​ 10,946 Other accrued expenses and current liabilities ​ 8,118 ​ 7,087 Operating lease liabilities, current ​ 1,523 ​ 1,720 Total current liabilities ​ 33,413 ​ 20,871 Operating lease liabilities, non-current ​ 30,050 ​ 30,860 Share repurchase liability ​ 1,234 ​ 1,771 Total liabilities ​ 64,697 ​ 53,502 Commitments and contingencies (Note 7) ​ ​ Redeemable convertible preferred stock, $ 0.0001 par value; 202,643,727 and 89,016,578 shares authorized as of June 30, 2024 and December 31, 2023, respectively; 168,489,871 and 85,960,088 shares issued and outstanding as of June 30, 2024 and December 31, 2023, respectively; aggregate liquidation preference of $ 629,540 and $ 370,540 as of June 30, 2024 and December 31, 2023, respectively ​ 639,237 ​ 375,370 Stockholders’ deficit: ​ ​ Common stock, $ 0.0001 par value; 225,000,000 and 125,000,000 Class A shares authorized as of June 30, 2024 and December 31, 2023, respectively; 2,741,498 and 2,675,979 Class A shares issued and outstanding as of June 30, 2024 and December 31, 2023, respectively; 168,489,897 and 85,960,088 Class B shares authorized as of June 30, 2024 and December 31, 2023, respectively; no Class B shares issued and outstanding as of June 30, 2024 and December 31, 2023 ​ 1 ​ 1 Additional paid-in capital ​ 31,920 ​ 25,055 Accumulated other comprehensive (loss) income ​ ( 1 ) ​ 2 Accumulated deficit ​ ( 470,675 ) ​ ( 364,318 ) Total stockholders’ deficit ​ ( 438,755 ) ​ ( 339,260 ) Total liabilities, redeemable convertible preferred stock and stockholders’ deficit ​ $ 265,179 ​ $ 89,612 ​ The accompanying notes are an integral part of these condensed consolidated financial statements. ​ 3 Table of Contents ALUMIS INC. CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS AND COMPREHENSIVE LOSS ​ (Unaudited) ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended June 30, Six Months Ended June 30, ​ (in thousands, except share and per share amounts) 2024 2023 2024 2023 Operating expenses: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Research and development expenses, including related party expenses of $ 213 , $ 429 , $ 571 and $ 754 for the three and six months ended June 30, 2024 and 2023, respectively ​ $ 48,565 ​ $ 32,848 ​ $ 90,526 ​ $ 65,283 ​ General and administrative expenses ​ 7,575 ​ 4,775 ​ 13,207 ​ 9,000 ​ Total operating expenses ​ 56,140 ​ 37,623 ​ 103,733 ​ 74,283 ​ Loss from operations ​ ( 56,140 ) ​ ( 37,623 ) ​ ( 103,733 ) ​ ( 74,283 ) ​ Other income (expense): ​ ​ ​ ​ ​ Interest income ​ 1,977 ​ 913 ​ 2,831 ​ 1,558 ​ Change in fair value of derivative liability ​ ( 2,311 ) ​ 432 ​ ( 5,406 ) ​ 432 ​ Other income (expenses), net ​ ( 34 ) ​ ( 11 ) ​ ( 49 ) ​ ( 23 ) ​ Total other income (expense), net ​ ( 368 ) ​ 1,334 ​ ( 2,624 ) ​ 1,967 ​ Net loss ​ $ ( 56,508 ) ​ $ ( 36,289 ) ​ $ ( 106,357 ) ​ $ ( 72,316 ) ​ Other comprehensive income (loss): ​ ​ ​ ​ ​ Unrealized gain (loss) on marketable securities, net ​ — ​ 30 ​ ( 3 ) ​ 130 ​ Net loss and other comprehensive loss ​ $ ( 56,508 ) ​ $ ( 36,259 ) ​ $ ( 106,360 ) ​ $ ( 72,186 ) ​ Net loss per share attributable to Class A common stockholders, basic and diluted ​ $ ( 23.10 ) ​ $ ( 17.13 ) ​ $ ( 44.17 ) ​ $ ( 35.14 ) ​ Weighted-average Class A common shares outstanding, basic and diluted ​ 2,446,022 ​ 2,117,861 ​ 2,408,037 ​ 2,058,178 ​ ​ The accompanying notes are an integral part of these condensed consolidated financial statements. ​ 4 Table of Contents ALUMIS INC. CONDENSED CONSOLIDATED STATEMENTS OF REDEEMABLE CONVERTIBLE PREFERRED STOCK AND STOCKHOLDERS’ DEFICIT ​ (Unaudited) ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Redeemable ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Accumulated ​ ​ ​ ​ ​ ​ ​ Convertible ​ ​ ​ ​ ​ ​ Additional Other ​ ​ Total ​ ​ Preferred Stock ​ ​ Common Stock Paid-In Comprehensive Accumulated Stockholders’ (in thousands, except share amounts) Shares Amount ​ Shares Amount Capital Income (Loss) Deficit Deficit Balance at December 31, 2023 85,960,088 ​ $ 375,370 ​ ​ 2,675,979 ​ $ 1 ​ $ 25,055 ​ $ 2 ​ $ ( 364,318 ) ​ $ ( 339,260 ) Issuance of Series C redeemable convertible preferred stock in March 2024 for cash, net of derivative liability of $ 8,913 and issuance costs of $ 382 41,264,891 ​ 120,205 ​ ​ — ​ — ​ — ​ — ​ — ​ — Issuance of common stock upon exercise of stock options and early exercise of stock options — ​ — ​ ​ 3,186 ​ — ​ 29 ​ — ​ — ​ 29 Vesting of early exercised stock options — ​ — ​ ​ — ​ — ​ 494 ​ — ​ — ​ 494 Vesting of restricted shares of common stock — ​ — ​ ​ — ​ — ​ 6 ​ — ​ — ​ 6 Stock-based compensation expense — ​ — ​ ​ — ​ — ​ 2,657 ​ — ​ — ​ 2,657 Other comprehensive loss, net — ​ — ​ ​ — ​ — ​ — ​ ( 3 ) ​ — ​ ( 3 ) Net loss — ​ — ​ ​ — ​ — ​ — ​ — ​ ( 49,849 ) ​ ( 49,849 ) Balance at March 31, 2024 127,224,979 ​ $ 495,575 ​ ​ 2,679,165 ​ $ 1 ​ $ 28,241 ​ $ ( 1 ) ​ $ ( 414,167 ) ​ $ ( 385,926 ) ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Issuance of Series C redeemable convertible preferred stock for cash and settlement of the derivative liability of $ 14,319 , net of issuance costs of $ 157 41,264,892 ​ 143,662 ​ ​ — ​ — ​ — ​ — ​ — ​ — Issuance of common stock upon exercise of stock options and early exercise of stock options — ​ — ​ ​ 62,333 ​ — ​ 287 ​ — ​ — ​ 287 Vesting of early exercised stock options — ​ — ​ ​ — ​ — ​ 253 ​ — ​ — ​ 253 Vesting of restricted shares of common stock — ​ — ​ ​ — ​ — ​ 6 ​ — ​ — ​ 6 Stock-based compensation expense — ​ — ​ ​ — ​ — ​ 3,133 ​ — ​ — ​ 3,133 Net loss — ​ — ​ ​ — ​ — ​ — ​ — ​ ( 56,508 ) ​ ( 56,508 ) Balance at June 30, 2024 168,489,871 ​ $ 639,237 ​ ​ 2,741,498 ​ $ 1 ​ $ 31,920 ​ $ ( 1 ) ​ $ ( 470,675 ) ​ $ ( 438,755 ) ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Redeemable ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Accumulated ​ ​ ​ ​ ​ ​ ​ Convertible ​ ​ ​ ​ ​ ​ Additional Other ​ ​ Total ​ ​ Preferred Stock ​ ​ Common Stock Paid-In Comprehensive Accumulated Stockholders’ (in thousands, except share amounts) Shares Amount ​ Shares Amount Capital (Loss) Income Deficit Deficit Balance at December 31, 2022 67,960,088 ​ $ 285,473 ​ ​ 2,642,334 ​ $ 1 ​ $ 14,209 ​ $ ( 127 ) ​ $ ( 209,325 ) ​ $ ( 195,242 ) Vesting of early exercised stock options — ​ — ​ ​ — ​ — ​ 694 ​ — ​ — ​ 694 Vesting of restricted shares of common stock — ​ — ​ ​ — ​ — ​ 5 ​ — ​ — ​ 5 Repurchase of unvested common stock shares issued upon early exercised stock options — ​ — ​ ​ ( 13,369 ) ​ — ​ — ​ — ​ — ​ — Stock-based compensation expense ​ — ​ ​ — ​ ​ — ​ ​ — ​ ​ 1,831 ​ ​ — ​ ​ — ​ ​ 1,831 Other comprehensive income, net — ​ — ​ ​ — ​ — ​ — ​ 100 ​ — ​ 100 Net loss — ​ — ​ ​ — ​ — ​ — ​ — ​ ( 36,027 ) ​ ( 36,027 ) Balance at March 31, 2023 67,960,088 ​ $ 285,473 ​ ​ 2,628,965 ​ $ 1 ​ $ 16,739 ​ $ ( 27 ) ​ $ ( 245,352 ) ​ $ ( 228,639 ) ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Issuance of Series B-2 and Series B-2A redeemable convertible preferred stock for cash, net of $ 2,112 derivative liability and $ 208 issuance costs ​ 10,722,340 ​ ​ 51,290 ​ ​ — ​ ​ — ​ ​ — ​ ​ — ​ ​ — ​ ​ — Issuance of Series B-2A redeemable convertible preferred stock for cash ​ 1,277,660 ​ ​ 6,389 ​ ​ — ​ ​ — ​ ​ — ​ ​ — ​ ​ — ​ ​ — Issuance of common stock upon exercise of stock options and early exercise of stock options ​ — ​ ​ — ​ ​ 18,395 ​ ​ — ​ ​ 71 ​ ​ — ​ ​ — ​ ​ 71 Vesting of early exercised stock options — ​ — ​ ​ — ​ — ​ 559 ​ — ​ — ​ 559 Vesting of restricted shares of common stock — ​ — ​ ​ — ​ — ​ 6 ​ — ​ — ​ 6 Stock-based compensation expense ​ — ​ ​ — ​ ​ — ​ ​ — ​ ​ 1,909 ​ ​ — ​ ​ — ​ ​ 1,909 Other comprehensive income, net — ​ — ​ ​ — ​ — ​ — ​ 30 ​ — ​ 30 Net loss — ​ — ​ ​ — ​ — ​ — ​ — ​ ( 36,289 ) ​ ( 36,289 ) Balance at June 30, 2023 79,960,088 ​ $ 343,152 ​ ​ 2,647,360 ​ $ 1 ​ $ 19,284 ​ $ 3 ​ $ ( 281,641 ) ​ $ ( 262,353 ) ​ The accompanying notes are an integral part of these condensed consolidated financial statements. ​ 5 Table of Contents ALUMIS INC. CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS ​ (Unaudited) ​ ​ ​ ​ ​ ​ ​ ​ ​ Six Months Ended June 30, (in thousands) ​ 2024 2023 Cash flows from operating activities ​ ​ Net loss ​ $ ( 106,357 ) ​ $ ( 72,316 ) Adjustments to reconcile net loss to net cash used in operating activities: ​ ​ Stock-based compensation ​ 5,790 ​ 3,740 Non-cash lease expense ​ 12 ​ 1,520 Depreciation and amortization ​ 1,518 ​ 240 Net accretion of discounts on marketable securities ​ ( 507 ) ​ ( 470 ) Loss on disposal of fixed assets ​ 5 ​ — Change in fair value of derivative liability ​ 5,406 ​ ( 432 ) Changes in operating assets and liabilities: ​ ​ Research and development prepaid expenses ​ ( 10,540 ) ​ 2,081 Other prepaid expenses and other assets ​ ( 382 ) ​ ( 157 ) Accounts payable ​ 7,788 ​ 666 Research and development accrued expenses ​ 3,638 ​ 2,276 Other accrued expenses and current liabilities ​ ( 1,912 ) ​ ( 245 ) Operating lease liabilities ​ ( 1,007 ) ​ 95 Net cash used in operating activities ​ ( 96,548 ) ​ ( 63,002 ) Cash flows from investing activities ​ ​ Maturities of marketable securities ​ 8,000 ​ 66,500 Purchases of marketable securities ​ ( 58,964 ) ​ ( 8,340 ) Purchases of property and equipment ​ ( 587 ) ​ ( 1,120 ) Net cash (used in) provided by investing activities ​ ( 51,551 ) ​ 57,040 Cash flows from financing activities ​ ​ Proceeds from issuance of redeemable convertible preferred stock and derivative liability, net of issuance costs ​ 258,461 ​ 59,791 Proceeds from issuance of common stock upon exercise of stock options ​ 537 ​ 171 Payments of deferred offering costs ​ ( 1,787 ) ​ — Repurchase of unvested common stock shares issued upon early exercised stock options ​ — ​ ( 51 ) Net cash provided by financing activities ​ 257,211 ​ 59,911 Net increase in cash, cash equivalents and restricted cash ​ 109,112 ​ 53,949 Cash, cash equivalents and restricted cash at beginning of period ​ 47,133 ​ 26,954 Cash, cash equivalents and restricted cash at end of period ​ $ 156,245 ​ $ 80,903 Supplemental disclosures: ​ ​ Right-of-use assets obtained in exchange for operating lease liabilities ​ $ — ​ $ 14,255 Property and equipment acquired through tenant improvement allowance ​ $ — ​ $ 11,537 Vesting of early exercised stock options and unvested restricted shares of common stock ​ $ 759 ​ $ 1,264 Purchases of property and equipment in other accrued expenses and current liabilities ​ $ 716 ​ $ 411 Recognition of derivative liability upon issuance of redeemable convertible preferred stock ​ $ 8,913 ​ $ 2,112 Settlement of derivative liability upon issuance of redeemable convertible preferred stock ​ $ ( 14,319 ) ​ $ — Deferred offering costs in accounts payable and other accrued expenses and current liabilities ​ $ 2,559 ​ $ 90 Reconciliation of cash, cash equivalents and restricted cash: ​ ​ Cash and cash equivalents ​ $ 155,108 ​ $ 79,560 Restricted cash ​ 113 ​ 206 Restricted cash, non-current ​ 1,024 ​ 1,137 Total cash, cash equivalents and restricted cash ​ $ 156,245 ​ $ 80,903 ​ The accompanying notes are an integral part of these condensed consolidated financial statements. ​ ​ 6 Table of Contents ALUMIS INC. NOTES TO THE CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (Unaudited) 1. Organization and Nature of the Business Organization and Business Alumis Inc. (the “Company”) is a clinical stage biopharmaceutical company focused on identifying, acquiring, and accelerating the development and commercialization of transformative medicines for autoimmune disorders. The Company leverages its proprietary precision data analytics platform, biological insights, and a team of experts with deep experience in precision medicine drug discovery, development, and immunology, to create medicines that significantly improve the lives of patients by replacing broad immunosuppression with targeted therapies. The Company was founded on January 29, 2021 as a Delaware corporation under the name FL2021-001, Inc. FL2021-001, Inc.’s name was changed to Esker Therapeutics, Inc. on March 8, 2021 and to Alumis Inc. on January 6, 2022. The Company is headquartered in South San Francisco, California. Reverse Stock Split On June 19, 2024, the board of directors approved, and on June 20, 2024, the Company effected, a reverse stock split of the shares of the Company’s outstanding common stock at a ratio of 1 -for-4.675 (the “Reverse Stock Split”). The number of authorized shares and par value per share were not adjusted as a result of the Reverse Stock Split. All references to shares, options to purchase common stock, share amounts, per share amount, and related information contained in the condensed consolidated financial statements have been retrospectively adjusted to reflect the effect of the Reverse Stock Split for all periods presented. The shares of common stock underlying outstanding stock options and other equity instruments were proportionately reduced and the respective exercise prices, if applicable, were proportionately increased in accordance with the terms of the agreements governing such securities. In addition, the conversion ratios for each series of the Company’s redeemable convertible preferred stock, which were automatically convertible into shares of common stock upon the closing of the Company’s initial public offering (the “IPO”) of common stock, were proportionally adjusted. Initial Public Offering and Concurrent Private Placement On June 28, 2024, the Company’s Registration Statement on Form S-1 for its IPO was declared effective, and on July 1, 2024, the Company completed its IPO, pursuant to which it issued and sold 13,125,000 shares of its common stock at $ 16.00 price per share to the public. Net proceeds from the IPO were approximately $ 193.2 million, after deducting underwriting discounts and commissions and other offering costs totaling approximately $ 16.8 million. In connection with the IPO, an existing investor and a holder of more than 5 % of the Company’s capital stock, purchased an additional 2,500,000 shares of the Company’s common stock at the IPO price per share for a total of $ 40.0 million in a private placement transaction (the “Concurrent Private Placement”). The closing of the Concurrent Private Placement was contingent on the closing of the IPO. The sale of such shares is not registered under the Securities Act of 1933, as amended (the “Securities Act”), and as such, the shares may not be offered or sold absent registration or an applicable exemption from registration. The shares sold in connection with the Concurrent Private Placement are subject to existing resale registration rights and are subject to a 180-day lock-up agreement with the underwriters in the IPO. The Concurrent Private Placement closed on July 17, 2024. Immediately prior to the closing of the IPO on July 1, 2024, all of the shares of the Company’s redeemable convertible preferred stock then outstanding converted into 28,855,656 shares of Class A common stock and 7,184,908 shares of Class B common stock at a 1 -for-4.675 conversion ratio (the “Preferred Stock Conversion”). All outstanding Class A common stock shares and all outstanding Class B common stock shares were redesignated immediately thereafter into the same number of shares of common stock and non-voting common stock, respectively (the “Common Stock Reclassification”). 7 Table of Contents ALUMIS INC. NOTES TO THE CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (Continued) (unaudited) 1. Organization and Nature of the Business (Continued) Initial Public Offering and Concurrent Private Placement (Continued) The condensed consolidated financial statements as of June 30, 2024, including share and per share amounts, do not give effect to the Preferred Stock Conversion, the Common Stock Reclassification, the IPO or the Concurrent Private Placement, as they occurred subsequent to June 30, 2024. In connection with the closing of the Company’s IPO, the Company increased the authorized number of shares to 500,000,000 shares of common stock and 50,000,000 shares of preferred stock. The authorized number of common stock shares includes voting common stock of 492,815,092 shares and non-voting common stock of 7,184,908 shares. Liquidity The Company has incurred negative operating cash flows and significant losses from operations since its inception. For the three and six months ended June 30, 2024, the Company incurred net losses of $ 56.5 million and $ 106.4 million, respectively. Cash used in operating activities was $ 96.5 million and $ 63.0 million for the six months ended June 30, 2024 and 2023, respectively. As of June 30, 2024, the Company had an accumulated deficit of $ 470.7 million. The Company has historically financed its operations primarily through issuance of common stock and redeemable convertible preferred stock and convertible promissory notes in private placements, and most recently, through an initial public offering and concurrent private placement. The Company expects to continue to incur substantial losses for the foreseeable future, and its ability to achieve and sustain profitability will depend on the successful development, approval, and commercialization of any product candidates it may develop, and on the achievement of sufficient revenue to support its cost structure. The Company may never achieve profitability and, unless and until it does, it will need to continue to raise additional capital. As of June 30, 2024, the Company had cash, cash equivalents and marketable securities of $ 209.5 million. In July 2024, in connection with the closing of the IPO and the Concurrent Private Placement, the Company received an additional $ 233.2 million in aggregate net cash proceeds, net of underwriting discounts and commissions and other offering costs. Management believes that its existing cash, cash equivalents and marketable securities together with the IPO and the Concurrent Private Placement proceeds will be sufficient to fund its current operating plan for at least the next 12 months from the date of issuance of these condensed consolidated financial statements. ​ Additional funds are necessary to maintain current operations and to continue research and development activities. The Company’s management plans to monitor expenses and may raise additional capital through a combination of public and private equity, debt financings, strategic alliances, and licensing arrangements. The Company’s ability to access capital when needed is not assured and, if capital is not available to the Company when, and in the amounts, needed, on the terms which are favorable, the Company could be required to delay, scale back, or abandon some or all of its development programs and other operations, which could materially harm the Company’s business, financial condition and results of operations. ​ 2. Summary of Significant Accounting Policies and Basis of Presentation The significant accounting policies and estimates used in the preparation of the accompanying condensed consolidated financial statements are described in the Company’s audited consolidated financial statements for the year ended December 31, 2023 included in the Company’s final prospectus for its IPO filed pursuant to Rule 424(b)(4) under the Securities Act with the Securities and Exchange Commission (the “SEC”), on June 28, 2024 (the “Prospectus”). There have been no material changes in the Company’s significant accounting policies during the three months ended June 30, 2024. 8 Table of Contents ALUMIS INC. NOTES TO THE CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (Continued) (unaudited) 2. Summary of Significant Accounting Policies and Basis of Presentation (Continued) Basis of Presentation The condensed consolidated financial statements and accompanying notes are unaudited and have been prepared in accordance with accounting principles generally accepted in the United States of America (“U.S. GAAP”) and applicable rules and regulations of the SEC regarding interim financial reporting and do not contain all information that is included in the annual financial statements and notes thereto of the company. Prior to their dissolution, the Company’s condensed consolidated financial statements included the accounts of FronThera U.S. Holdings, Inc. and FronThera U.S. Pharmaceuticals LLC, two wholly owned subsidiaries, and all intercompany transactions were eliminated. FronThera U.S. Holdings, Inc. was dissolved on April 8, 2024 and FronThera U.S. Pharmaceuticals LLC was dissolved on March 14, 2024. The condensed consolidated interim financial statements have been prepared on the same basis as the audited annual financial statements and, in the opinion of management, reflect all adjustments, which include only normal recurring adjustments necessary for the fair statement of the Company’s financial position as of June 30, 2024 and the results of its operations and its cash flows for the three and six months ended June 30, 2024 and 2023. The condensed balance sheet as of December 31, 2023 was derived from audited annual consolidated financial statements but does not include all disclosures required by U.S. GAAP. The results of operations for the three and six months ended June 30, 2024 are not necessarily indicative of the results of operations to be expected for the full year or for any other subsequent interim period. Any reference in these notes to applicable guidance is meant to refer to the authoritative U.S. GAAP as found in the Accounting Standards Codification (“ASC”) and Accounting Standards Updates (“ASU”) of the Financial Accounting Standards Board (“FASB”). Use of Estimates The preparation of financial statements in conformity with U.S. GAAP requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities, the disclosure of contingent assets and liabilities at the date of the financial statements and the reported amounts of expenses during the reporting period. On an ongoing basis, the Company evaluates estimates and assumptions, including but not limited to those related to the fair value of its common and redeemable convertible preferred stock, the fair value of derivative liability, stock-based compensation expense, accruals for research and development expenses and the valuation of deferred tax assets. Management bases its estimates on historical experience and on various other assumptions that are believed to be reasonable under the circumstances, the results of which form the basis for making judgments about the carrying values of assets and liabilities that are not readily apparent from other sources. Actual results may differ materially from those estimates. Segment and Geographical Information The Company operates and manages its business as one reportable and operating segment, which is the business of developing medicines for autoimmune disorders. The chief executive officer, who is the chief operating decision maker, reviews financial information on an aggregate basis for purposes of allocating resources and evaluating financial performance. All of the Company’s long-lived assets are located in the United States. Concentration of Credit Risk Financial instruments which potentially subject the Company to concentration of credit risk consist primarily of cash, investments in marketable securities and restricted cash. The Company maintains bank deposits in federally insured financial institutions and these deposits exceed federally insured limits. To date, the Company has not experienced any losses on its deposits of cash and periodically evaluates the creditworthiness of its financial institutions. 9 Table of Contents ALUMIS INC. NOTES TO THE CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (Continued) (unaudited) 2. Summary of Significant Accounting Policies and Basis of Presentation (Continued) The Company also invests in money market funds and U.S. treasuries, which are subject to certain credit risks. The Company mitigates the risks by investing in high-grade instruments, limiting its exposure to any one issuer and monitoring the ongoing creditworthiness of the financial institutions and issuers. The Company has not experienced any loss of principal on its financial instruments. Risks and Uncertainties The Company is subject to certain risks and uncertainties, including, but not limited to, changes in any of the following areas that the Company believes could have a material adverse effect on the future financial position or results of operations: the Company’s ability to advance the development of its proprietary precision data analytics platform, timing and ability to advance its product candidates through preclinical and clinical development; costs and timelines associated with the manufacturing of clinical supplies; regulatory approval, market acceptance of, and reimbursement for, any product candidates the Company may develop; performance of third-party vendors; competition from pharmaceutical or other biotechnology companies with greater financial resources or expertise; protection of intellectual property; litigation or claims against the Company based on intellectual property or other factors; and its ability to attract and retain employees necessary to support its growth. The Company’s business and operations may be affected by worldwide economic conditions, which may continue to be impacted by global macroeconomic challenges, such as the effects of the ongoing military conflicts in Ukraine, Israel, and the Middle East, tensions in U.S.-China relations, uncertainty in the markets, including disruptions in the banking industry, the COVID-19 pandemic and inflationary trends. Fiscal year 2023 was marked by significant market uncertainty and increasing inflationary pressures. These market dynamics continue into 2024, and these and similar adverse market conditions may negatively impact the Company’s business, financial position and results of operations. Deferred Finance Issuance Costs Deferred finance issuance costs, consisting of legal, accounting and other third-party fees directly relating to in-process equity financings or offerings are capitalized. The deferred finance issuance costs will be offset against offering proceeds upon the completion of the financing or the offering. In the event the financing or the offering is terminated or delayed, deferred finance issuance costs will be expensed immediately as a charge to general and administrative expenses in the condensed consolidated statements of operations and comprehensive loss. The Company had $ 4.3 million in deferred finance issuance costs capitalized and included in other long-term assets in its condensed consolidated balance sheet as of June 30, 2024, which will be reclassified to equity upon the closing of the IPO in the third quarter of 2024. There were no deferred finance issuance costs capitalized and included in other long-term assets in the condensed consolidated balance sheet as of December 31, 2023. Recent Accounting Pronouncements From time to time, new accounting pronouncements are issued by the FASB or other standard setting bodies and adopted by the Company as of the specified effective date. The Company qualifies as an “emerging growth company” as defined in the Jumpstart Our Business Startups Act of 2012, as amended (the “JOBS Act”), and has elected not to “opt out” of the extended transition related to complying with new or revised accounting standards, which means that when a standard is issued or revised and it has different application dates for public and nonpublic companies, the Company will adopt the new or revised standard at the time nonpublic companies adopt the new or revised standard and will do so until such time that the Company either (i) irrevocably elects to “opt out” of such extended transition period or (ii) no longer qualifies as an emerging growth company. The Company may choose to early adopt any new or revised accounting standards whenever such early adoption is permitted for nonpublic companies. 10 Table of Contents ALUMIS INC. NOTES TO THE CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (Continued) (unaudited) 2. Summary of Significant Accounting Policies and Basis of Presentation (Continued) Recently Issued and Not Yet Adopted Accounting Pronouncements In November 2023, the FASB issued ASU 2023-07, Segment Reporting (Topic 280): Improvements to Reportable Segment Disclosures . This ASU requires public entities to disclose information about their reportable segments’ significant expenses and other segment items on an interim and annual basis. Public entities with a single reportable segment are required to apply the disclosure requirements in ASU 2023-07, as well as all existing segment disclosures and reconciliation requirements in ASC 280 on an interim and annual basis. ASU 2023-07 is effective for fiscal years beginning after December 15, 2023, and for interim periods within fiscal years beginning after December 15, 2024, with early adoption permitted. The Company is currently evaluating the impact of adopting ASU 2023-07 on its condensed consolidated financial statements. In December 2023, the FASB issued ASU No. 2023-09, Income Taxes (Topic 740): Improvements to Income Tax Disclosures , which requires the disclosure of specific categories in the rate reconciliation and greater disaggregation for income taxes paid. This standard is effective for annual periods beginning after December 15, 2024 and should be adopted prospectively with the option to be adopted retrospectively. The Company is currently evaluating the impact of this standard on its disclosure in its condensed consolidated financial statements. In March 2024, the FASB issued ASU No. 2024-02, Codification Improvements - Amendments to Remove References to the Concepts Statements . The amendments in ASU 2024-02 clarify and simplify references to certain concept statements within U.S. GAAP. ASU 2024-02 is effective for fiscal years beginning after December 15, 2024, with early application permitted. The Company is currently evaluating the impact of the adoption of this standard on its condensed consolidated financial statements. ​ ​ 3. Fair Value Measurements The Company discloses and recognizes the fair value of its assets and liabilities using a hierarchy that prioritizes the inputs to valuation techniques used to measure fair value. The guidance establishes three levels of the fair value hierarchy as follows: Level 1—Quoted prices in active markets for identical assets or liabilities. Level 2—Observable inputs other than Level 1 prices, such as quoted prices for similar assets or liabilities, quoted prices in markets that are not active, or other inputs that are observable or can be corroborated by observable market data for substantially the full term of the assets or liabilities. Level 3—Unobservable inputs that are supported by little or no market activity and that are significant to the fair value of the assets or liabilities. Assets and liabilities measured at fair value are classified in their entirety based on the lowest level of input that is significant to the fair value measurement. The Company’s assessment of the significance of a particular input to the fair value measurement in its entirety requires management to make judgments and consider factors specific to the asset or liability. The Company recognizes transfers into and out of levels within the fair value hierarchy in the period in which the actual event or change in circumstances that caused the transfer occurs. The Company’s financial instruments consist of Level 1, Level 2 and Level 3 financial instruments. Changes in the ability to observe valuation inputs may result in a reclassification of levels of certain securities within the fair value hierarchy. Level 1 financial instruments are comprised of money market funds and U.S. treasuries. Level 2 financial instruments are comprised of U.S. treasuries. Usually, short term marketable securities are considered Level 2 when their fair values are determined using inputs that are observable in the market or can be derived principally from or corroborated by observable market data such as pricing for similar securities, recently executed transactions, cash flow models with yield curves, and 11 Table of Contents ALUMIS INC. NOTES TO THE CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (Continued) (unaudited) 3. Fair Value Measurements (Continued) benchmark securities. In addition, Level 2 financial instruments are valued using comparisons to like-kind financial instruments and models that use readily observable market data as their basis. Level 3 financial instruments include derivative liabilities issued in May 2023 and settled in October 2023 in connection with the closing of the second tranche of the Series B-2 and B-2A redeemable convertible preferred stock financing, and issued in March 2024 and settled in May 2024 in connection with the closing of the second tranche of the Series C redeemable convertible preferred stock financing. The following tables represent the Company’s fair value hierarchy for financial assets and liabilities measured at fair value on a recurring basis as of June 30, 2024 and December 31, 2023 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Fair Value Measurements as of June 30, 2024 ​ Level 1 Level 2 Level 3 Total Assets: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Cash equivalents ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Money market funds ​ $ 104,826 ​ $ — ​ $ — ​ $ 104,826 U.S. treasuries ​ 42,072 ​ — ​ — ​ 42,072 Marketable securities ​ ​ ​ ​ ​ U.S. treasuries ​ 27,006 ​ 27,417 ​ — ​ 54,423 Total assets ​ $ 173,904 ​ $ 27,417 ​ $ — ​ $ 201,321 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Fair Value Measurements as of December 31, 2023 ​ Level 1 Level 2 Level 3 Total Assets: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Cash equivalents ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Money market funds ​ $ 21,310 ​ $ — ​ $ — ​ $ 21,310 U.S. treasuries ​ ​ 2,000 ​ ​ — ​ ​ — ​ ​ 2,000 Marketable securities ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ U.S. treasuries ​ 1,958 ​ 998 ​ — ​ 2,956 Total assets ​ $ 25,268 ​ $ 998 ​ $ — ​ $ 26,266 ​ The derivative liability issued in May 2023 in connection with the closing of the second tranche of the Series B-2 and B-2A redeemable convertible preferred stock financing was a freestanding financial instrument and represented the Company’s obligation to issue additional shares of Series B-2 and B-2A redeemable convertible preferred stock at a fixed price upon the approval by the Company’s board of directors. In connection with the Series C redeemable convertible preferred stock financing in March 2024, the Company issued to investors two freestanding financial instruments: the Series C second tranche option liability and the put right option liability. The Company estimated their fair value using a Black-Scholes option pricing model weighted by the probability of occurring. The Company used the intrinsic value calculation to estimate the fair value of the Series C second tranche option liability and the put right option liability upon settlement. Significant estimates and assumptions impacting the derivative liability fair value included the probability of each option exercise, redeemable convertible preferred stock fair value, estimated stock volatility and the expected term. 12 Table of Contents ALUMIS INC. NOTES TO THE CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (Continued) (unaudited) 3. Fair Value Measurements (Continued) The following tables provide a range of assumptions used in the valuation of the derivative liabilities for the six months ended June 30, 2024 and 2023: ​ ​ ​ ​ ​ ​ ​ ​ Six Months Ended June 30, ​ 2024 2023 Expected term (in years) ​ 0.16 – 0.36 0.26 – 0.41 ​ Expected volatility ​ 55.1 % – 59.9 % ​ 67.63 % – 83.25 % ​ Risk-free interest rate ​ 5.4 % – 5.5 % ​ 5.23 % – 5.44 % ​ Expected dividend yield ​ 0 % ​ 0 % ​ Probability of event occurring ​ 0 % – 100 % ​ 30 % ​ ​ The following table provides a roll-forward of the fair value of the Company’s Level 3 financial instrument, the derivative liabilities, for the six months ended June 30, 2024 and 2023 (in thousands): ​ ​ ​ ​ ​ Balance as of January 1, 2024 $ — Fair value upon issuance ​ 8,913 Changes in fair value ​ 5,406 Fair value upon settlement ​ ( 14,319 ) Balance as of June 30, 2024 $ — ​ ​ ​ ​ ​ Balance as of January 1, 2023 $ — Fair value upon issuance ​ 2,112 Changes in fair value ​ ( 432 ) Balance as of June 30, 2023 ​ $ 1,680 ​ There were no transfers between Level 1, Level 2 or Level 3 categories for the three and six months ended June 30, 2024 and 2023. ​ 4. Marketable Securities Marketable securities, which are classified as available-for-sale marketable securities, consisted of the following as of June 30, 2024 and December 31, 2023 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Gross Gross Fair Value as of ​ ​ Amortized Cost ​ Unrealized ​ Unrealized ​ June 30, ​ ​ Basis ​ Gains ​ Losses ​ 2024 Short-term marketable securities: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ U.S. treasuries ​ $ 54,424 ​ $ — ​ $ ( 1 ) ​ $ 54,423 Total short-term marketable securities ​ $ 54,424 ​ $ — ​ $ ( 1 ) ​ $ 54,423 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Gross Gross Fair Value as of ​ ​ Amortized Cost ​ Unrealized ​ Unrealized ​ December 31, ​ ​ Basis ​ Gains ​ Losses ​ 2023 Short-term marketable securities: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ U.S. treasuries ​ $ 2,954 ​ $ 2 ​ $ — $ 2,956 Total short-term marketable securities ​ $ 2,954 ​ $ 2 ​ $ — $ 2,956 ​ All marketable securities held as of June 30, 2024 and December 31, 2023, had contractual maturities of less than one year. ​ 13 Table of Contents ALUMIS INC. NOTES TO THE CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (Continued) (unaudited) 4. Marketable Securities (Continued) As of June 30, 2024 and December 31, 2023, no significant facts or circumstances were present to indicate a deterioration in the creditworthiness of the issuers of the marketable securities, and the Company has no requirement or intention to sell these securities before maturity or recovery of their amortized cost basis. The Company considered the current and expected future economic and market conditions and determined that its investments were not significantly impacted. For all securities with a fair value less than its amortized cost basis, the Company determined the decline in fair value below amortized cost basis to be immaterial and non-credit related, and therefore no allowance for losses has been recorded. During the three and six months ended June 30, 2024 and 2023, the Company did no t recognize any impairment losses on its investments. ​ 5. Balance Sheet Components Other Prepaid Expenses and Current Assets Other prepaid expenses and current assets consisted of the following as of June 30, 2024 and December 31, 2023 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ June 30, December 31, ​ ​ 2024 ​ 2023 Tax receivable ​ $ 614 ​ $ 614 Interest receivable ​ ​ 283 ​ ​ 108 Prepaid subscriptions ​ ​ 797 ​ ​ 703 Other ​ 318 ​ 206 Total other prepaid expenses and current assets ​ $ 2,012 ​ $ 1,631 ​ Property and Equipment, net Property and equipment, net consisted of the following as of June 30, 2024 and December 31, 2023 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Estimated Useful Life June 30, December 31, ​ ​ (in years) ​ 2024 ​ 2023 Leasehold improvements Shorter of useful life or lease term ​ $ 17,618 ​ $ 17,592 Laboratory equipment 5 ​ ​ 4,798 ​ ​ 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 ​ ​ ​ 25,096 ​ 23,849 Less: Accumulated depreciation and amortization ​ ​ ​ ( 2,923 ) ​ ( 1,408 ) Total property and equipment, net ​ ​ ​ $ 22,173 ​ $ 22,441 ​ Depreciation and amortization expense was $ 0.8 million and $ 0.1 million for the three months ended June 30, 2024 and 2023, respectively, and $ 1.5 million and $ 0.2 million for the six months ended June 30, 2024 and 2023, respectively. 14 Table of Contents ALUMIS INC. NOTES TO THE CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (Continued) (unaudited) 5. Balance Sheet Components (Continued) Other Accrued Expenses and Current Liabilities Other accrued expenses and current liabilities consist of the following as of June 30, 2024 and December 31, 2023 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ June 30, December 31, ​ ​ 2024 ​ 2023 Accrued personnel and related expenses ​ $ 3,355 ​ $ 5,585 Accrued professional services ​ 4,213 ​ 1,093 Accrued other expenses ​ 550 ​ 409 Total other accrued expenses and current liabilities ​ $ 8,118 ​ $ 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 three months ended June 30, 2024 and 2023, the Company recognized $ 0.2 million and $ 0.4 million as research and development expenses under the service agreement, respectively. For the six months ended June 30, 2024 and 2023, the Company recognized $ 0.6 million and $ 0.8 million as research and development expenses under the service agreement, respectively. Accrued expenses under the service agreement were zero as of June 30, 2024 and were less than $ 0.1 million as of December 31, 2023. ​ 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, that 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, this lease was modified to reduce the contractual lease term to terminate in 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 additional 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 was received in the year ended December 31, 2022, and $ 16.7 million was received in the year ended December 31, 2023, and was accounted for as a reduction to lease payments. At the commencement date, future lease payments totaled $ 37.9 million, 15 Table of Contents ALUMIS INC. NOTES TO THE CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (Continued) (unaudited) 7. Commitments and Contingent Liabilities (Continued) Operating Leases (Continued) including $ 54.6 million in gross fixed payments less $ 16.7 million in lease incentives expected to be 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. The Company recorded the leasehold improvements in property and equipment, net in the condensed consolidated balance sheets as of June 30, 2024 and December 31, 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. The Company maintains letters of credit on these leases in the amount of $ 1.1 million as of June 30, 2024 and December 31, 2023. The lease letters of credit are reflected on the Company’s condensed consolidated balance sheets in restricted cash, current and restricted cash, noncurrent as of June 30, 2024 and December 31, 2023. The components of lease costs were as follows (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended Six Months Ended ​ ​ ​ June 30, ​ June 30, ​ ​ 2024 2023 2024 2023 ​ Operating lease costs ​ $ 835 ​ $ 1,279 ​ $ 1,711 ​ $ 2,551 ​ Variable lease costs ​ 326 ​ 70 ​ 656 ​ 116 ​ Total lease costs ​ $ 1,161 ​ $ 1,349 ​ $ 2,367 ​ $ 2,667 ​ ​ Supplemental cash flow information related to the operating leases were as follows (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ Six Months Ended ​ ​ ​ June 30, ​ ​ 2024 2023 ​ Cash payments included in the measurement of operating lease liabilities ​ $ 2,745 ​ $ 935 ​ ​ Weighted-average remaining lease term and incremental borrowing rate for the operating leases were as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ June 30, ​ December 31, ​ ​ 2024 2023 ​ Weighted-average remaining lease term (years) 9.1 ​ 9.5 ​ Weighted-average incremental borrowing rate 11.4 % 11.4 % ​ 16 Table of Contents ALUMIS INC. NOTES TO THE CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (Continued) (unaudited) 7. Commitments and Contingent Liabilities (Continued) Operating Leases (Continued) Future minimum lease payments under non-cancelable leases as of June 30, 2024, were as detailed below (in thousands): ​ ​ ​ ​ ​ 2024 (remainder of the year) ​ $ 2,554 2025 ​ ​ 4,959 2026 ​ 5,125 2027 ​ 5,296 2028 ​ 5,474 Thereafter ​ 27,515 Total undiscounted lease payments ​ 50,923 Less: Imputed interest ​ ( 19,350 ) Total operating lease liabilities ​ $ 31,573 ​ 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, for up to an aggregate of $ 70.0 million payable for clinical milestones, and for up to an aggregate of $ 50.0 million payable for approval milestones, all related to technology acquired under the agreement. The Company incurred and paid a $ 37.0 million milestone in 2022 for the first administration of ESK-001 to a patient enrolled in a Phase 2 clinical trial of ESK-001, which was recorded as research and development expense in the consolidated statement of operations and comprehensive loss for the year ended December 31, 2022. In July 2024, the Company met its milestone in connection with the first administration of ESK-001 to a patient enrolled in a Phase 3 clinical trial of ESK-001 and became obligated to pay $ 23.0 million, which is expected to be recorded as research and development expenses in the third quarter of 2024, when probable. No other milestones were achieved or probable as of June 30, 2024. Research and Development Agreements The Company enters into various agreements in the ordinary course of business, such as those with suppliers, clinical research organizations, contract manufacturing organizations 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 condensed consolidated 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 17 Table of Contents ALUMIS INC. NOTES TO THE CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (Continued) (unaudited) 7. Commitments and Contingent Liabilities (Continued) Guarantees and Indemnifications (Continued) 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 June 30, 2024 and December 31, 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 issuance 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 contains 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. 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 issuance 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 issuance 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 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 are two freestanding financial instruments and estimated their 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 issuance costs. Accordingly, the derivative liability was settled, and the 18 Table of Contents ALUMIS INC. NOTES TO THE CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (Continued) (unaudited) 8. Redeemable Convertible Preferred Stock (Continued) Company reclassified the derivative liability, remeasured at fair value of $ 14.3 million, into redeemable convertible preferred stock. The Series Seed and Series A redeemable convertible preferred stock are collectively referred to as the “Junior Redeemable Convertible Preferred Stock”. The Series B, Series B-1, Series B-2, Series B-2A, Series C and Series C-1 redeemable convertible preferred stock are collectively referred to as the “Senior Redeemable Convertible Preferred Stock”. The Company’s redeemable convertible preferred stock as of June 30, 2024 and December 31, 2023, consisted of the following: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ June 30, 2024 ​ ​ ​ ​ 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 1,778,830 1,778,830 ​ 8,894 ​ 8,928 Series C redeemable convertible preferred stock ​ 82,529,809 ​ 82,529,783 ​ ​ 259,000 ​ ​ 263,867 Series C-1 redeemable convertible preferred stock ​ 32,375,000 ​ — ​ ​ — ​ ​ — Total redeemable convertible preferred stock 202,643,727 168,489,871 ​ $ 629,540 ​ $ 639,237 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ 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 ​ 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 common stock and non-voting common stock (see Note 1) and are no longer outstanding. The significant rights and obligations of the Company’s redeemable convertible preferred stock are as follows: Liquidation Preference In the event of the liquidation, dissolution or winding up of the Company, or a deemed liquidation event, including a merger or consolidation, or a sale or other disposition of all or substantially all of the Company’s assets, the holders of shares of the Senior Redeemable Convertible Preferred Stock are entitled to receive, before any payments are made to the holders of the Junior Redeemable Convertible Preferred Stock and holders of common stock, an amount per share equal to the greater of (i) the Series B, Series B-1, Series B-2, Series B-2A, Series C and Series C-1 original issuance price of 19 Table of Contents ALUMIS INC. NOTES TO THE CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (Continued) (unaudited) 8. Redeemable Convertible Preferred Stock (Continued) Liquidation Preference (Continued) $ 5.00 , $ 4.00 , $ 5.00 , $ 5.00 , $ 3.13826 and $ 4.00 , respectively, plus any dividends declared but unpaid, or (ii) such amount per share as would have been payable had all shares of the applicable series of Senior Redeemable Convertible Preferred Stock been converted into common stock immediately prior to such liquidation, dissolution, winding up or deemed liquidation. If the proceeds are insufficient to pay the holders of shares of Senior Redeemable Convertible Preferred Stock their full liquidation preference, then the proceeds available for distribution are payable ratably among the holders of the Senior Redeemable Convertible Preferred Stock in proportion to the full preferential amount that each such holder is entitled to receive. After the distributions to the holders of the Senior Redeemable Convertible Preferred Stock have been paid in full, the holder of shares of Junior Redeemable Convertible Preferred Stock will be entitled to receive, prior to and in preference to any distributions of the assets of the Company to the holders of common stock, an amount equal to the greater of (i) the Series Seed and Series A original issuance price of $ 1.00 and $ 4.00 , respectively, plus any dividends declared but unpaid, or (ii) such amount per share as would have been payable had all shares of such series of Junior Redeemable Convertible Preferred Stock been converted into common stock immediately prior to such liquidation, dissolution, winding up or deemed liquidation. If the proceeds are insufficient to pay the holder of share of Junior Redeemable Convertible Preferred Stock their full liquidation preference, then the proceeds available for distribution are payable ratably among the holders of the Junior Redeemable Convertible Preferred Stock in proportion to the full preferential amount that each such holder is entitled to receive. After the distributions described above have been paid in full, the remaining assets of the Company available for distribution to its stockholders will be distributed among the holders of shares of common stock, pro rata based on the number of shares held by each such holder. Conversion Each share of Series B-2 redeemable convertible preferred stock is convertible at the option of a holder into one share of Series B-2A redeemable convertible preferred stock. Each share of Series B-2A redeemable convertible preferred stock is convertible at the option of a holder into one share of Series B-2 redeemable convertible preferred stock. Each share of redeemable convertible preferred stock is convertible at the option of a holder into shares of Class A common stock or Class B common stock at a conversion rate, which is the redeemable convertible preferred stock original issuance price per share divided by the conversion price in effect at the time of conversion. No shares of Series C and Series C-1 redeemable convertible preferred stock may be converted into shares of common stock at any time during the period commencing on March 4, 2024 and ending on the first to occur of (i) the Second Tranche Series C Closing, (ii) the day after December 31, 2024, (iii) a termination event as specified in the Series C stock purchase agreement and (iv) such other time as determined by the board of directors in its good faith judgment. The conversion price is initially equal to the redeemable convertible preferred stock original issuance price, and is subject to adjustments for recapitalization, dilutive issuances, stock dividends, stock splits, and other distributions. No adjustment in the conversion price of any series of redeemable convertible preferred stock will be made as the result of the issuance or deemed issuance of additional shares of common stock if the Company receives written notice from a majority of the then outstanding shares of such series of redeemable convertible preferred stock agreeing that no such adjustment will be made as the result of the issuance or deemed issuance of such additional shares of common stock. As of June 30, 2024 and December 31, 2023, the conversion price as adjusted for the reverse stock split was $ 4.68 per share for the Series Seed redeemable convertible preferred stock, $ 14.67 per share for the Series C redeemable convertible preferred stock, $ 18.70 per share for the Series A redeemable convertible preferred stock, Series B-1 redeemable convertible preferred stock and Series C-1 redeemable convertible 20 Table of Contents ALUMIS INC. NOTES TO THE CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (Continued) (unaudited) 8. Redeemable Convertible Preferred Stock (Continued) Conversion (Continued) preferred stock, and $ 23.38 per share for the Series B redeemable convertible preferred stock, Series B-2 redeemable convertible preferred stock and Series B-2A redeemable convertible preferred stock. All outstanding shares of redeemable convertible preferred stock are automatically converted into shares of Class A common stock, provided that, a holder of shares of redeemable convertible preferred stock may elect, upon written notice to the Company at least seven days prior to a qualified public offering, to have all or a portion of its shares of redeemable convertible preferred stock automatically convert into shares of Class B common stock at the then effective conversion rate, upon the earlier of: (i) the closing of the sale of shares of common stock to the public at a price of at least $ 17.61 , in a firm-commitment underwritten public offering pursuant to an effective registration statement under the Securities Act of 1933, as amended, resulting in at least $ 75.0 million of proceeds to the Company, net of underwriting discount and commissions, and in connection with such offering the common stock is listed for trading on the Nasdaq Stock Market’s National Market, the New York Stock Exchange or another exchange or marketplace approved by the board of directors, or (ii) the date and time, or the occurrence of an event, specified by a vote or a written consent of (a) the holders of a majority of outstanding shares of redeemable convertible preferred stock, voting together as a single class and on an as-converted basis, and (b) the holders of a majority of Series C and Series C-1 redeemable convertible preferred stock, voting together as a single class and on an as-converted basis. Dividend Rights The Company cannot declare, pay or set aside any dividends on shares of any other class or series of capital stock of the Company (other than dividends on shares of common stock payable in shares of common stock), unless the holders of the redeemable convertible preferred stock then outstanding will first receive, or simultaneously receive, a dividend on each outstanding share of redeemable convertible preferred stock in an amount at least equal to (i) in the case of a dividend on common stock or any class or series that is convertible into common stock, the product of (a) the dividend payable on each share of such series determined as if all shares of such series had been converted into common stock and (b) the number of shares of common stock issuable upon conversion of a share of redeemable convertible preferred stock, calculated on the record date for determination of holders entitled to receive such dividend or (ii) in the case of a dividend on any class or series that is not convertible into common stock, at a rate per share of redeemable convertible preferred stock determined by (a) dividing the amount of the dividend payable on each share of such class or series of capital stock by the original issuance price of such class or series of capital stock (subject to appropriate adjustment in the event of any stock dividend, stock split, combination or other similar recapitalization with respect to such class or series) and (b) multiplying such fraction by an amount equal to the applicable original issue price. If the Company declares, pays or sets aside, on the same date, a dividend on shares of more than one class or series of capital stock of the Company, the dividend payable to the holders of redeemable convertible preferred stock will be calculated based upon the dividend on the class or series of capital stock that would result in the highest redeemable convertible preferred stock dividend. No dividends were declared and paid or payable for the for the six months ended June 30, 2024 and year ended December 31, 2023. Voting Rights Each holder of outstanding shares of redeemable convertible preferred stock is entitled to cast the number of votes equal to the number of whole shares of common stock into which the shares of redeemable convertible preferred stock held by such holder are convertible. Holders of redeemable convertible preferred stock vote together with the holders of common stock as a single class and on an as-converted to common stock basis. Holders of Series B-2A redeemable convertible preferred stock have no voting rights for election of directors or for the size of the board. 21 Table of Contents ALUMIS INC. NOTES TO THE CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (Continued) (unaudited) 8. Redeemable Convertible Preferred Stock (Continued) Election of Directors At any time when at least 1,875,000 shares of Series A redeemable convertible preferred stock are outstanding, the holders of the shares of Series A redeemable convertible preferred stock, voting as a separate class on an as-converted to common stock basis, are entitled to elect one director of the Company. Election of Directors (Continued) At any time when at least 10,050,000 shares of the voting Series B, Series B-1, Series B-2 are outstanding, the holders of the shares of the Series B, Series B-1, Series B-2, voting as a separate class on an as-converted to common stock basis, are entitled to elect two directors of the Company. At any time when at least 10,316,222 shares of Series C and Series C-1 redeemable convertible preferred stock are outstanding, the holders of the shares of Series C and Series C-1 redeemable convertible preferred stock, voting as a separate class on an as-converted to common stock basis, are entitled to elect two directors of the Company. The holders of the shares of common stock, voting as a separate class, are entitled to elect one director of the Company. The holders of common stock and redeemable convertible preferred stock, voting together as a single class on an as-converted basis, are entitled to elect all remaining members of the board of directors, if any. Redemption The redeemable convertible preferred stock is recorded in mezzanine equity because while it is not mandatorily redeemable, it will become redeemable at the option of the preferred stockholders upon the occurrence of certain deemed liquidation events that are considered not solely within the Company’s control. 9. Common Stock As of June 30, 2024, the Company was authorized to issue 225,000,000 shares of Class A common stock and 168,489,897 shares of Class B common stock, both with par values of $ 0.0001 per share (Class A common stock and Class B common stock, collectively referred to as “common stock”). As of June 30, 2024 and December 31, 2023, there were no shares of Class B common stock outstanding. The holders of Class A and Class B common stock have the same rights except that Class B common stock do not have voting rights, except as may be required by law. Each holder of Class B common stock has a right to convert each share of Class B common stock to one share of Class A common stock. The Company cannot issue shares of Class B common stock other than upon conversion of redeemable convertible preferred stock. At any time following the Company’s registration of any class of equity securities under the Exchange Act, the holders of shares of Class B common stock may not convert a number of shares of Class B common stock into shares of Class A common stock in excess of that number of shares of Class B 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 Class A common stock (including shares of Class A common stock issuable upon conversion of the redeemable convertible preferred stock). Such maximum percentage may be increased or decreased to such other percentage as any holder of outstanding shares of Class B common stock may designate in writing upon 61 days’ prior written notice. 22 Table of Contents ALUMIS INC. NOTES TO THE CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (Continued) (unaudited) 9. Common Stock (Continued) Common stock reserved for issuance, on an as-converted basis, consisted of the following as of June 30, 2024 and December 31, 2023: ​ ​ ​ ​ ​ ​ ​ June 30, December 31, ​ ​ 2024 ​ 2023 Redeemable convertible preferred stock issued and outstanding 36,040,564 18,387,168 Outstanding and issued common stock options 8,725,148 5,096,086 Shares available for grant under 2024 Equity Incentive Plan ​ 7,693,365 ​ — Shares available for grant under 2024 Employee Stock Purchase Plan ​ 650,000 ​ — Shares available for grant under 2021 Stock Plan — 296,189 Shares available for grant under 2024 Performance Option Plan ​ 33,274 ​ — Total 53,142,351 23,779,443 ​ Common Stock Issued to Executives In February 2021, the Company issued 100,532 shares of 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. The holders have voting and dividends rights. The Company has the right to repurchase unvested shares 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 less than $ 0.1 million of stock-based compensation expense for the three and six months ended June 30, 2024 and 2023. The following table summarizes the activity for the Company’s restricted common stock for the six months ended June 30, 2024: ​ ​ ​ ​ ​ ​ ​ ​ ​ Weighted- ​ ​ ​ ​ Average ​ ​ Number of ​ Grant Date ​ ​ Shares ​ Fair Value Unvested as of December 31, 2023 29,322 ​ $ 2.90 Vested ( 12,567 ) ​ $ 2.90 Unvested as of June 30, 2024 16,755 ​ $ 2.90 ​ As of June 30, 2024, the remaining unamortized stock-based compensation expense of less than $ 0.1 million will be recognized over the remaining vesting period of 0.6 years. ​ 23 Table of Contents ALUMIS INC. NOTES TO THE CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (Continued) (unaudited) 10. Stock Compensation 2024 Equity Incentive Plan On June 27, 2024, the Company’s board of directors adopted, and its stockholders approved, the 2024 Equity Incentive Plan (the “2024 EIP”), which became effective on June 28, 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 Stock Plan (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 is a successor to the 2021 Plan and no further grants will be made under the 2021 Plan. 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 and ending in 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. No more than 43,888,017 shares of 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 incentive stock options (“ISOs”), non-statutory stock options (“NSOs”), restricted stock awards, restricted stock units (“RSUs”), stock appreciation rights, performance awards and other stock-based awards. Options under the 2024 EIP may be granted for periods of up to 10 years at exercise prices no less than the fair market value of common stock on the date of grant; provided, however, that the exercise price of an incentive stock option granted to a 10% stockholder may not be less than 110 % of the fair market value of the shares on the date of grant and such option may not be exercisable after the expiration of five years from the date of grant. Stock option grants under the 2024 EIP generally vest over four years . The grant date fair market value of all awards made under the 2024 EIP and all cash compensation paid by the Company to any non-employee director for services as a director in any fiscal year may not exceed $ 750,000 , increased to $ 1,000,000 in the fiscal year of their initial service as a non-employee director. In June 2024, the Company issued to certain directors and employees, including its executive officers, stock options to purchase an aggregate of 163,131 shares of its common stock with an exercise price equal to the IPO’s price of $ 16.00 per share, under the 2024 EIP. As of June 30, 2024, there were 7,693,365 shares authorized and available for issuance under the 2024 EIP. 2024 Employee Stock Purchase Plan In June 2024, the 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 capital 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 a discount through payroll deductions of up to 15 % of the employee’s eligible compensation. At the end of each offering period, employees are able to purchase shares at 85 % of the lower of the fair market value of our common stock at the beginning of the offering period or at the end of each applicable offering period. 24 Table of Contents ALUMIS INC. NOTES TO THE CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (Continued) (unaudited) 10. Stock Compensation (Continued) 2024 Performance Option Plan In May 2024, the Company’s board of directors adopted and the shareholders 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. 2021 Stock Plan Prior to the IPO, the Company granted stock awards under the 2021 Plan, adopted in February 2021. Subsequent to the adoption of the 2024 EIP in June 2024, no additional shares were available for issuance under the 2021 Plan and any stock options granted under the 2021 Plan that were subsequently forfeited would be made available for issuance under the 2024 EIP. The terms of the 2021 Plan permit option holders to exercise options before their options are vested. The shares of common stock granted upon early exercise that have not yet vested are subject to repurchase by the Company in the event of termination of the holder’s continuous status as a service provider, at the price paid by the holder. Stock Option Repricing In March 2024, the Company’s board of directors approved the repricing of all outstanding options as of March 29, 2024, which have 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 will be recognized over the remainder of the original requisite service period. ​ 25 Table of Contents ALUMIS INC. NOTES TO THE CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (Continued) (unaudited) 10. Stock Compensation (Continued) Stock Option Activity The following table summarizes the Company’s option activity under the 2021 Plan and the 2024 EIP for the six months ended June 30, 2024. The table includes early exercised shares as part of 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 8.50 ​ $ 15,033 Options granted 1,959,928 ​ $ 12.25 ​ ​ ​ ​ ​ Options exercised ( 65,519 ) ​ $ 8.20 ​ ​ ​ $ 343 Options forfeited or expired ( 112,753 ) ​ $ 10.01 ​ ​ ​ ​ Outstanding and expected to vest as of June 30, 2024 6,877,742 ​ $ 9.49 8.53 ​ $ 26,690 Exercisable as of June 30, 2024 6,714,611 ​ $ 9.33 8.49 ​ $ 26,690 ​ The total fair value of shares vested for the six months ended June 30, 2024 and 2023 was $ 5.5 million and $ 4.6 million, respectively. The weighted-average grant date fair value of options granted was $ 10.47 and $ 9.36 for the six months ended June 30, 2024 and 2023, respectively. During the six months ended June 30, 2024 and 2023, 65,519 options and 18,395 options were exercised with intrinsic values of $ 0.3 million and less than $ 0.1 million, respectively, and the Company received $ 0.5 million and $ 0.2 million, respectively, in proceeds from issuance of common stock upon exercise of stock options, respectively. The following table summarizes the Company’s option activity under the 2024 POP for the six months ended June 30, 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 — ​ $ — ​ — ​ $ — Options granted 1,880,680 ​ $ 10.19 ​ ​ ​ Options exercised — ​ $ — ​ ​ ​ ​ $ — Options forfeited or expired ( 33,274 ) ​ $ 10.19 ​ ​ ​ ​ Outstanding and expected to vest as of June 30, 2024 1,847,406 ​ $ 10.19 ​ 9.85 ​ $ 5,743 Exercisable as of June 30, 2024 — ​ $ — ​ — ​ $ — ​ ​ 26 Table of Contents ALUMIS INC. NOTES TO THE CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (Continued) (unaudited) 10. Stock Compensation (Continued) Stock Option Valuation The fair value of stock options granted under the 2024 EIP and the 2021 Plan for the six months ended June 30, 2024 and 2023 was estimated using the Black-Scholes option pricing model with the following assumptions: ​ ​ ​ ​ ​ ​ ​ ​ Six Months Ended June 30, ​ 2024 2023 Expected term (in years) ​ 5.92  –  6.08 5.95  –  6.63 Volatility ​ 103.65 % – 105.69 % 98.08 % – 102.54 % Risk-free interest rate ​ 4.20 % –  4.48 % 3.66 % –  3.98 % Dividend yield ​ 0 % 0 % ​ 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 did 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 any trading history for the Company’s common stock. The Company will continue to analyze the historical stock price volatility and expected term assumption as more historical data for the Company’s common stock becomes available. Risk-Free Interest Rate The risk-free interest rate assumption is based on the U.S. Treasury instruments whose term was consistent with the expected term of the Company’s stock options. Dividends The Company has not paid any cash dividends on common stock since inception and does not anticipate paying any dividends in the foreseeable future. Consequently, an expected dividend yield of zero was used. Common Stock Fair Value The fair market value of the Company’s common stock is 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 is consistent with the methods outlined in the Practice Aid. 27 Table of Contents ALUMIS INC. NOTES TO THE CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (Continued) (unaudited) 10. Stock Compensation (Continued) Common Stock Fair Value (Continued) 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 on and after May 2023, the Company utilized a hybrid method that combines 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 option pricing model 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 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. The Company also considers the amount of time between the independent third-party valuation dates and the grant dates and performs 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. Stock Options Granted Under the 2024 POP Stock options granted under the 2024 POP 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 are 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 6.00 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. 28 Table of Contents ALUMIS INC. NOTES TO THE CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (Continued) (unaudited) 10. Stock Compensation (Continued) Stock Options Granted Under the 2024 POP (Continued) The Company estimated fair value of stock options issued under the 2024 POP of $ 18.0 million will be recognized after the performance condition is probable over the longer of (i) the explicit service period of the service condition of 3.0 years or (ii) the derived service period between 1.4 years to 2.1 years. As the IPO was not considered probable until it closed on July 1, 2024, no stock-based compensation expense is recognized for the three and six months ended June 30, 2024. Early Exercise of Employee 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 condensed consolidated balance sheets. As of June 30, 2024 and December 31, 2023, there was $ 1.2 million and $ 1.8 million share repurchase liability related to the unvested shares, respectively. The following table summarizes the activity for the Company’s early exercised shares for the six months ended June 30, 2024: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Weighted- ​ ​ ​ ​ Average ​ ​ Number of ​ Exercise Price ​ Shares Per Share Unvested as of December 31, 2023 327,100 ​ $ 5.33 Early exercised 25,034 ​ $ 8.84 Vested ( 122,373 ) ​ $ 6.10 Unvested as of June 30, 2024 229,761 ​ $ 5.30 ​ Stock-Based Compensation Expense The following table summarizes the stock-based compensation expense granted to employees and non-employees for the three and six months ended June 30, 2024 and 2023 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended June 30, ​ Six Months Ended June 30, ​ ​ 2024 2023 2024 2023 ​ Research and development ​ $ 1,641 ​ $ 1,065 ​ $ 3,085 ​ $ 2,067 ​ General and administrative ​ 1,492 ​ 844 ​ 2,705 ​ 1,673 ​ Total stock-based compensation expense ​ $ 3,133 ​ $ 1,909 ​ $ 5,790 ​ $ 3,740 ​ ​ The following table summarizes the stock-based compensation expense related to the following equity-based awards for the three and six months ended June 30, 2024 and 2023 (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended June 30, ​ Six Months Ended June 30, ​ ​ 2024 2023 2024 2023 ​ Stock options ​ $ 3,115 ​ $ 1,891 ​ $ 5,754 ​ $ 3,704 ​ Restricted stock awards ​ 18 ​ 18 ​ 36 ​ 36 ​ Total stock-based compensation expense ​ $ 3,133 ​ $ 1,909 ​ $ 5,790 ​ $ 3,740 ​ ​ Stock-based compensation expense related to non-employee awards was immaterial for all periods presented. As of June 30, 2024, there was unrecognized stock-based compensation expense of $ 61.7 million related to issued stock-based award which the Company expects to recognize over a weighted-average period of 3.12 years. 29 Table of Contents ALUMIS INC. NOTES TO THE CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (Continued) (unaudited) 11. Net Loss Per Share Attributable to Class A Common Stockholders The following table sets forth the computation of the basic and diluted net loss per share attributable to Class A common stockholders for the three and six months ended June 30, 2024 and 2023 (in thousands, except share and per share amounts): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended June 30, ​ Six Months Ended June 30, ​ ​ 2024 2023 2024 2023 ​ Numerator: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Net loss ​ $ ( 56,508 ) ​ $ ( 36,289 ) ​ $ ( 106,357 ) ​ $ ( 72,316 ) ​ Denominator: ​ ​ ​ ​ ​ ​ Weighted average Class A common shares outstanding ​ 2,700,082 ​ 2,636,985 ​ 2,689,624 ​ 2,635,952 ​ Less: Weighted-average Class A common shares subject to repurchase ​ ( 254,060 ) ​ ( 519,124 ) ​ ( 281,587 ) ​ ( 577,774 ) ​ Weighted-average Class A common shares outstanding, basic and diluted ​ ​ 2,446,022 ​ ​ 2,117,861 ​ ​ 2,408,037 ​ ​ 2,058,178 ​ Net loss per share attributable to Class A common stockholders, basic and diluted ​ $ ( 23.10 ) ​ $ ( 17.13 ) ​ $ ( 44.17 ) ​ $ ( 35.14 ) ​ ​ The following outstanding potentially dilutive shares were excluded from the computation of diluted net loss per share attributable to Class A common stockholders for the periods presented, because including them would have been anti-dilutive (on an as-converted basis): ​ ​ ​ ​ ​ ​ ​ June 30, 2024 June 30, 2023 Redeemable convertible preferred stock issued and outstanding ​ 36,040,564 ​ 17,103,749 Common stock options issued and outstanding 8,725,148 4,640,139 Unvested restricted common stock and early exercised stock options 246,516 483,544 Total 45,012,228 22,227,432 ​ ​ 12. 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 during the three and six months ended June 30, 2024 and 2023. ​ 13. Subsequent Events In July 2024, the Company closed its IPO and Concurrent Private Placement and received aggregate net proceeds of $ 233.2 million. 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. Refer to Note 1 for details. In July 2024, the Company met a clinical milestone under the FronThera Acquisition and is obligated to pay $ 23.0 million. Refer to Note 7 for details. ​ ​ 30 Table of Contents