Amendment: SEC Form SCHEDULE 13D/A filed by Alumis Inc.

The address of the principal place of business for each of Fund VI, FCM VI, Fund V, Labs Co-Invest, FCM V, Opportunity Fund V, FCOM V, Labs Fund I, FLM I and Tananbaum is c/o Foresite Capital Management, LLC, 900 Larkspur Landing Circle, Suite 150, Larkspur, CA 94939. The address of the principal place of business for each of Labs Affiliates and Labs is c/o Foresite Labs, LLC, 101 Mission Street, 12th Floor, San Francisco, CA 94105.

The principal occupation of each of the Reporting Persons is the venture capital investment business. The principal business of each of Fund VI, Fund V, Labs Co-Invest, Opportunity Fund V, Labs Fund I and Labs Affiliates is to make investments in private and public companies. The principal business of FCM VI is to serve as the general partner of Fund VI, the principal business of FCM V is to serve as the general partner of Fund V and the managing member of Labs Co-Invest, the principal business of FCOM V is to serve as the general partner of Opportunity Fund V and the principal business of FLM I is to serve as the general partner of Labs Fund I. The principal business of Labs is to engage in the business of data science and incubation in the fields of life sciences and healthcare. Tananbaum is the managing member of each of FCM VI, FCM V, FCOM V and FLM I. Tananbaum is also a manager of Labs and a member of the board of directors of the Issuer.

During the last five years, none of the Reporting Persons has been convicted in any criminal proceeding (excluding traffic violations or similar misdemeanors).

During the last five years, none of the Reporting Persons has been a party to a civil proceeding of a judicial or administrative body of competent jurisdiction and as a result of such proceeding was or is subject to a judgment, decree or final order enjoining future violations of, or prohibiting or mandating activities subject to, federal or state securities laws or finding any violation with respect to such laws.

Each of Fund VI, Fund V, Opportunity Fund V and Labs Fund I is a Delaware limited partnership. Each of FCM VI, FCM V, FCOM V, FLM I, Labs Co-Invest, Labs Affiliates and Labs is a Delaware limited liability company. Tananbaum is a U.S. citizen.

Acquisition of Common Stock In February 2021, Labs Affiliates purchased an aggregate of 5,500,000 shares of Common Stock from the Issuer at a purchase price of $0.0001 per share, or $550 in the aggregate. Conversion of Simple Agreements for Future Equity (SAFEs) and Direct Purchase of Series Seed Redeemable Convertible Preferred Stock In February 2021, Fund V and Labs Co-Invest purchased an aggregate of 10,000,000 shares of Series Seed Redeemable Convertible Preferred Stock from the Issuer at a purchase price of $1.00 per share, or $10 million in the aggregate. The purchase price consisted of (i) $7,381,810.80 new cash investment by Fund V and the cancellation of $1,709,089.20 in SAFEs held by Fund V converted in connection with such financing, and (ii) $738,189.20 new cash investment by Labs Co-Invest and the cancellation of $170,910.80 in SAFEs held by Labs Co-Invest converted in connection with such financing. Direct Purchase of Series A Redeemable Convertible Preferred Stock In March 2021, Fund V purchased 5,250,000 shares of Series A Redeemable Convertible Preferred Stock and Opportunity Fund V purchased 2,250,000 shares of Series A Redeemable Convertible Preferred Stock at a purchase price of $4.00 per share, or $30.0 million in the aggregate. Convertible Promissory Notes In March 2021, the Issuer issued convertible promissory notes to Fund V, Opportunity V and Labs Fund I with a total principal amount of $30.0 million in exchange for $30.0 million in cash. In August 2021, the Issuer issued additional convertible promissory notes to Labs Fund I with a total principal amount of $1.5 million in exchange for $1.5 million in cash. In September 2021, the Issuer amended and restated all outstanding convertible promissory notes held by Fund V, Opportunity V and Labs Fund I and issued an additional convertible promissory note to Labs Fund I with a total principal amount of $6.0 million in exchange for $6.0 million in cash. Series B-1 Redeemable Convertible Preferred Stock Financing In December 2021, convertible notes held by Fund V, Opportunity V and Labs Fund I automatically converted into an aggregate 9,760,088 shares of Series B-1 Redeemable Convertible Preferred Stock of the Issuer at a conversion price of $4.00 per share, resulting in the cancellation of the Issuer's indebtedness of $39,040,356.18 in the aggregate. As a result, Fund V acquired 2,618,356 shares of Series B-1 Redeemable Convertible Preferred Stock of the Issuer, Opportunity Fund V acquired 2,618,356 shares of Series B-1 Redeemable Convertible Preferred Stock of the Issuer and Labs Fund I acquired 4,523,376 shares of Series B-1 Redeemable Convertible Preferred Stock of the Issuer. Direct Purchase of Series B-2 Redeemable Convertible Preferred Stock In May 2023, Fund V purchased an aggregate of 1,939,643 shares of Series B-2 Redeemable Convertible Preferred Stock of the Issuer, Opportunity Fund V purchased an aggregate of 969,821 shares of Series B-2 Redeemable Convertible Preferred Stock of the Issuer, Labs Fund I purchased an aggregate of 969,821 shares of Redeemable Convertible Preferred Stock of the Issuer, and Fund VI purchased an aggregate of 969,821 shares of Redeemable Convertible Preferred Stock of the Issuer at a price of $5.00 per share, or $24,245,530 in the aggregate. In October 2023, Fund V purchased an aggregate of 969,821 shares of Series B-2 Redeemable Convertible Preferred Stock of the Issuer, Opportunity Fund V purchased an aggregate of 484,910 shares of Series B-2 Redeemable Convertible Preferred Stock of the Issuer, Labs Fund I purchased an aggregate of 484,911 shares of Redeemable Convertible Preferred Stock of the Issuer, and Fund VI purchased an aggregate of 484,910 shares of Redeemable Convertible Preferred Stock of the Issuer at a price of $5.00 per share, or $12,122,760 in the aggregate. Direct Purchase of Series C Redeemable Convertible Preferred Stock In March 2024, Fund V purchased an aggregate of 2,389,859 shares of Series C Redeemable Convertible Preferred Stock of the Issuer, Opportunity Fund V purchased an aggregate of 1,593,239 shares of Series C Redeemable Convertible Preferred Stock of the Issuer, Labs Fund I purchased an aggregate of 1,593,239 shares of Series C Redeemable Convertible Preferred Stock of the Issuer, and Fund VI purchased an aggregate of 3,983,098 shares of Series C Redeemable Convertible Preferred Stock of the Issuer at a price of $3.13826 per share, or $29,999,992.48 in the aggregate. In May 2024, Fund V purchased an aggregate of 2,389,859 shares of Series C Redeemable Convertible Preferred Stock of the Issuer, Opportunity Fund V purchased an aggregate of 1,593,239 shares of Series C Redeemable Convertible Preferred Stock of the Issuer, Labs Fund I purchased an aggregate of 1,593,239 shares of Series C Redeemable Convertible Preferred Stock of the Issuer, and Fund VI purchased an aggregate of 3,983,098 shares of Series C Redeemable Convertible Preferred Stock of the Issuer at a price of $3.13826 per share, or $29,999,992.48 in the aggregate. Reverse Stock Split and Conversion On June 20, 2024, the Issuer effected a 1-for-4.675 reverse stock split of its issued and outstanding Common Stock, as a result of which Fund V held 1,944,577 shares of Series Seed Redeemable Convertible Preferred Stock of the Issuer; Labs Co-Invest held 194,459 shares of Series Seed Redeemable Convertible Preferred Stock of the Issuer; Fund V held 1,122,994 shares of Series A Redeemable Convertible Preferred Stock of the Issuer; Opportunity Fund V held 481,283 shares of Series A Redeemable Convertible Preferred Stock of the Issuer; Fund V held 560,076 shares of Series B-1 Redeemable Convertible Preferred Stock of the Issuer; Opportunity Fund V held 560,076 shares of Series B-1 Redeemable Convertible Preferred Stock of the Issuer; Labs Fund I held 967,567 shares of Series B-1 Redeemable Convertible Preferred Stock of the Issuer; Fund V held 622,344 shares of Series B-2 Redeemable Convertible Preferred Stock of the Issuer; Opportunity Fund V held 311,172 shares of Series B-2 Redeemable Convertible Preferred Stock of the Issuer; Labs Fund I held 311,172 shares of Series B-2 Redeemable Convertible Preferred Stock of the Issuer; Fund VI held 311,172 shares of Series B-2 Redeemable Convertible Preferred Stock of the Issuer; Fund V held 1,022,398 shares of Series C Redeemable Convertible Preferred Stock of the Issuer; Opportunity Fund V held 681,598 shares of Series C Redeemable Convertible Preferred Stock of the Issuer; Labs Fund I held 681,598 shares of Series C Redeemable Convertible Preferred Stock of the Issuer; Fund VI held 1,703,998 shares of Series C Redeemable Convertible Preferred Stock of the Issuer; and Labs Affiliates held 1,176,470 shares of Common Stock of the Issuer. In connection with the closing of the Issuer's initial public offering on July 1, 2024 (the "Initial Offering"), each share of Series Seed Redeemable Convertible Preferred Stock, Series A Redeemable Convertible Preferred Stock, Series B-1 Redeemable Convertible Preferred Stock, Series B-2 Redeemable Convertible Preferred Stock and Series C Redeemable Convertible Preferred Stock automatically converted into one share of Common Stock. Purchase in Initial Offering In connection with the Initial Offering, Fund V purchased 312,500 shares of the Issuer's Common Stock from the underwriters for $16.00 per share, or $5,000,000.00 in the aggregate; and Fund VI purchased 2,187,500 shares of the Issuer's Common Stock from the underwriters for $16.00 per share, or $35,000,000.00 in the aggregate. Such purchases occurred pursuant to and on the terms set forth in the Issuer's Prospectus filed pursuant to Rule 424(b)(4) on June 28, 2024 with the Securities and Exchange Commission (File No. 333-280068) (the "Prospectus"). Open Market Purchase On May 2, 2025, Fund VI purchased 25,000 shares of the Issuer's Common Stock at a price of $4.62 per share, or $115,500 in the aggregate, in an open market purchase. On May 6, 2025, Fund VI purchased 20,000 shares of the Issuer's Common Stock at a price of $4.34 per share, or $86,800 in the aggregate, in an open market purchase. On November 17, 2025, Opportunity Fund V purchased (i) 50,000 shares of the Issuer's Common Stock at a price of $5.60 per share, or $280,000 in the aggregate, in an open market purchase and (ii) 150,000 shares of the Issuer's Common Stock at a price of $5.59 per share, or $838,500 in the aggregate, in an open market purchase On November 18, 2025, Opportunity Fund V purchased 117,374 shares of the Issuer's Common Stock at a price of $6.19 per share, or $726,545.06 in the aggregate, in an open market purchase. On November 19, 2025, Opportunity Fund V purchased 190,500 shares of the Issuer's Common Stock at a price of $6.56 per share, or $1,249,680 in the aggregate, in an open market purchase. On November 21, 2025, Opportunity Fund V purchased 72,212 shares of the Issuer's Common Stock at a price of $7.38 per share, or $532,924.56 in the aggregate, in an open market purchase. Follow-on Offering The Issuer filed a Prospectus Supplement pursuant to Rule 424(b)(5) on January 8, 2026 with the Securities and Exchange Commission (the "2026 Prospectus Supplement") that details the Issuer's offering of 17,650,000 shares of Common Stock (the "Follow-on Offering"). On January 8, 2026, in connection with the Follow-on Offering, Fund V purchased 117,647 shares of the Issuer's Common Stock at a price of $17.00 per share, or $1,999,999 in the aggregate and Opportunity Fund V purchased 294,117 shares of the Issuer's Common Stock at a price of $17.00 per share, or $4,999,989 in the aggregate. Such purchases occurred pursuant to and on the terms set forth in the 2026 Prospectus Supplement. Source of Funds The source of the funds for all purchases and acquisitions by Fund VI, Fund V, Labs Co-Invest, Opportunity Fund V, Labs Fund I and Labs Affiliates was from working capital. No part of the purchase price was borrowed by Fund VI, Fund V, Labs Co-Invest, Opportunity Fund V, Labs Fund I and Labs Affiliates for the purpose of acquiring any securities discussed in this Item 3.

The Reporting Persons hold their securities of the Issuer for investment purposes. Depending on the factors discussed herein, the Reporting Persons may, from time to time, acquire additional shares of Common Stock and/or retain and/or sell all or a portion of the Common Stock held by the Reporting Persons in the open market or in privately negotiated transactions, and/or may distribute the Common Stock held by the Reporting Persons to their respective members or limited partners. Any actions the Reporting Persons might undertake will be dependent upon the Reporting Persons' review of numerous factors, including, among other things, the price levels of the Common Stock; general market and economic conditions; ongoing evaluation of the Issuer's business, financial condition, operations and prospects; the relative attractiveness of alternative business and investment opportunities; and other future developments. Except as set forth above, the Reporting Persons have no present plans or intentions which would result in or relate to any of the transactions described in subparagraphs (a) through (j) of Item 4 of Schedule 13D.

Regarding aggregate beneficial ownership, see Row 11 of the cover page of each Reporting Person. Regarding percentage beneficial ownership, see Row 13 of the cover page of each Reporting Person. Regarding sole power to vote shares, see Row 7 of the cover page of each Reporting Person. Regarding shared power to vote shares, see Row 8 of the cover page of each Reporting Person. Regarding sole power to dispose of shares, see Row 9 of the cover page of each Reporting Person. Regarding shared power to dispose of shares, see Row 10 of the cover page of each Reporting Person. The percentage listed in Row 13 for each Reporting Person was calculated based upon 95,819,723 shares of common stock of the Issuer outstanding as of May 21, 2025, as reported by the Issuer to the Reporting Persons.

See response to Item 5(a) above.

Except as set forth in Item 3 above, the Reporting Persons have not effected any transaction in the securities of the Issuer during the past 60 days.

Under certain circumstances set forth in the limited partnership agreement of each of Fund VI, Fund V, Opportunity Fund V and Labs Fund I and the limited liability company agreement of each of FCM VI, FCM V, FCOM V, FLM I, Labs Co-Invest, Labs Affiliates and Labs, the partners or members, as the case may be, of each of such entities may be deemed to have the right to receive dividends from, or the proceeds from the sale of, shares of the Issuer directly or indirectly owned by each such entity of which they are a partner or member.

Not applicable.

In connection with the issuance of the Series Seed Redeemable Convertible Preferred Stock, Series A Redeemable Convertible Preferred Stock, Series B-1 Redeemable Convertible Preferred Stock, Series B-2 Redeemable Convertible Preferred Stock and Series C Redeemable Convertible Preferred Stock of the Issuer, Fund VI, Fund V, Labs Co-Invest, Opportunity V, Labs Fund I and certain other investors entered into an Amended and Restated Investors' Rights Agreement dated March 4, 2024 (the "Rights Agreement"). The Rights Agreement grants to Fund VI, Fund V, Labs Co-Invest, Opportunity V, Labs Fund I and certain other parties thereto certain rights including demand registration rights, piggyback registration rights and Form S-3 registration rights. Such registration rights will expire, with respect to any particular stockholder, upon the earliest to occur of: (a) the closing of a Deemed Liquidation Event (as defined therein) (b) such time after consummation of the IPO (as defined therein) as Rule 144 or another similar exemption under the Securities Act (as defined therein) is available for the sale of all of such holder's shares without limitation during a three-month period without registration; or (c) the fifth anniversary of the IPO (as defined therein). The rights set forth in the Rights Agreement are more fully described in the Prospectus and incorporated herein by reference. Fund VI, Fund V, Labs Co-Invest, Opportunity V, Labs Fund I entered into a letter agreement with Morgan Stanley & Co, LLC, Leerink Partners LLC, Cantor Fitzgerald & Co., and Guggenheim Securities, LLC, as representatives of the underwriters, on March 4, 2024 (together, the "Lock-Up Agreements"). Pursuant to the Lock-Up Agreements, Fund VI, Fund V, Labs Co-Invest, Opportunity V, Labs Fund I and Tananbaum agreed that they would not, during the period ending 180 days after the date set forth on the Prospectus and subject to limited exceptions, (1) offer, pledge, sell, contract to sell, sell any option or contract to purchase, purchase any option or contract to sell, grant any option, right or warrant to purchase, lend, or otherwise transfer or dispose of, directly or indirectly, any shares of Common Stock beneficially owned (as such term is used in Rule 13d-3 of the Securities Exchange Act of 1934, as amended), or any other securities so owned convertible into or exercisable or exchangeable for Common Stock or (2) enter into any swap or other arrangement that transfers to another, in whole or in part, any of the economic consequences of ownership of the Common Stock, whether any such transaction described in clause (1) or (2) above is to be settled by delivery of Common Stock or such other securities, in cash or otherwise. Such Lock-Up Agreement is more fully described in the Prospectus and incorporated herein by reference. In connection with the Follow-On Offering, each of Tananbaum, Fund V and Opportunity Fund V entered into a lock-up agreement, pursuant to which each such party agreed, subject to certain exceptions, not to sell, transfer or otherwise convey certain of the Issuer's securities held by Fund V or Opportunity Fund V for 60 days following the date of the 2026 Prospectus Supplement. The terms and provisions of such lock-up agreement are described more fully in 2026 Prospectus Supplement, and the above summary is qualified by reference to such description and the full text of the lock-up agreement, a form of which is filed as Exhibit E to this Statement and is incorporated herein by reference. Tananbaum, in his capacity as a director of the Issuer, along with the other directors of the Issuer, entered into an Indemnification Agreement with the Issuer. Such Indemnification Agreement is more fully described in the Prospectus and incorporated herein by reference.

EXHIBIT A Agreement of Joint Filing. The undersigned hereby agree that a single Schedule 13D (or any amendment thereto) relating to the Common Stock of Alumis, Inc. shall be filed on behalf of each of the Reporting Persons. Note that copies of the applicable Agreement of Joint Filing are already on file with the appropriate agencies. EXHIBIT B Amended and Restated Investors' Rights Agreement, filed on June 7, 2024 as Exhibit 4.2 to the Issuer's Registration Statement on Form S-1 (File No. 333-80068), and incorporated herein by reference. EXHIBIT C Form of Lock-Up Agreement, filed as Exhibit A to the Underwriting Agreement filed on June 24, 2024 as Exhibit 1.1 to the Issuer's Amendment No. 2 to Form S-1 Registration Statement (File No. 333-80068), and incorporated herein by reference. EXHIBIT D Form of Indemnification Agreement, filed as Exhibit 10.10 to the Issuer's Amendment No. 2 to Form S-1 Registration Statement (File No. 333-80068) is incorporated herein by reference. EXHIBIT E Form of Lock-Up Agreement, filed as Exhibit A to the Underwriting Agreement filed on January 9, 2026 as Exhibit 1.1 to the Issuer's Form 8-K (File No. 001-42143), and incorporated herein by reference.