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SCHEDULE 13D/A 0000902664-24-004604 0001975990 XXXXXXXX LIVE 1 Common Stock, par value $0.0001 per share 02/06/2025 false 0001847367 022307102 ALUMIS INC. 280 EAST GRAND AVENUE SOUTH SAN FRANCISCO CA 94080 Gregory A. Brown 781-522-4007 AyurMaya Capital Management Company. LP 1000 Winter Street, Suite 4500 Waltham MA 02451 Ele Klein & Adriana Schwartz 212-756-2000 Schulte Roth & Zabel LLP 919 Third Avenue New York NY 10022 0001975990 N AyurMaya Capital Management Company, LP OO N DE 0.00 10645966.00 0.00 10645966.00 10645966.00 N 22.5 IA PN 0001548144 N David E. Goel OO N X1 0.00 10645966.00 0.00 10645966.00 10645966.00 N 22.5 IN HC Common Stock, par value $0.0001 per share ALUMIS INC. 280 EAST GRAND AVENUE SOUTH SAN FRANCISCO CA 94080 This Amendment No. 1 ("Amendment No. 1") amends and supplements the statement on Schedule 13D filed with the Securities and Exchange Commission on July 3, 2024 (the "Original Schedule 13D", and the Original Schedule 13D as amended, the "Schedule 13D"). This Amendment No. 1 supplements Items 4, 6 and 7 and amends and restates Items 5(a) - (c) as set forth below. Capitalized terms used herein and not otherwise defined in this Amendment No. 1 have the meanings set forth in the Schedule 13D. On February 6, 2025, the Issuer entered into an Agreement and Plan of Merger (the "Merger Agreement") with ACELYRIN, Inc., a Delaware corporation ("ACELYRIN"), and Arrow Merger Sub, Inc., a Delaware corporation and a direct wholly owned subsidiary of the Issuer ("Merger Sub"). Pursuant to the Merger Agreement, Merger Sub will be merged with and into ACELYRIN and ACELYRIN will continue as the surviving corporation and direct wholly owned subsidiary of the Issuer (the "Merger"), as more fully described in the Issuer's Current Report on Form 8-K filed with the Securities and Exchange Commission on February 6, 2025. In connection with the execution of the Merger Agreement, the Issuer entered into a Voting and Support Agreement (the "Voting Agreement") with the Investment Manager. Pursuant to the Voting Agreement, the Investment Manager has agreed, among other things, to (i) vote or cause to be voted all of its shares of Common Stock in favor of (A) the adoption of the Merger Agreement and approval of the transactions contemplated thereby, (B) any other proposals presented by ACELYRIN to its stockholders to effect or facilitate the transactions contemplated by the Merger Agreement and (C) any proposal to adjourn or postpone any meeting of the holders of shares of Common Stock at which the matters described in clause (A) are submitted for the consideration and vote of the holders of the shares of Common Stock to a later date if there are not sufficient votes for approval of such matters on the date on which the meeting is held; and (ii) against (A) any ACELYRIN acquisition proposal or any of the transactions contemplated thereby, (B) any action, proposal, transaction or agreement which could reasonably be expected to result in a breach of any covenant, representation or warranty, or any other obligation or agreement of ACELYRIN under the Merger Agreement or of the Investment Manager under the Voting Agreement and (C) any action, proposal, transaction, or agreement that could reasonably be expected to impede, interfere with, delay, discourage, adversely affect, or inhibit the timely consummation of the transactions contemplated by the Merger Agreement. The foregoing summary of the Voting Agreement does not purport to be complete and is qualified in its entirety by reference to the full text of the form of Voting Agreement, which has been filed as Exhibit 99.5 hereto and incorporated by reference herein. See rows (11) and (13) of the cover pages to this Schedule 13D for the aggregate number of shares of Common Stock and percentages of the shares of Common Stock beneficially owned by each Reporting Person. The percentages used in this Schedule 13D as of the date hereof are calculated based upon 47,222,419 shares of Common Stock outstanding as of January 31, 2025, as disclosed in the Merger Agreement attached as Exhibit 2.1 of the Issuer's Current Report on Form 8-K filed with the Securities and Exchange Commission on February 6, 2025. See rows (7) through (10) of the cover pages to this Schedule 13D for the number of shares of Common Stock as to which each Reporting Person has the sole or shared power to vote or direct the vote and sole or shared power to dispose or to direct the disposition. No transactions in the shares of Common Stock have been effected by the Reporting Persons during the past sixty (60) days. Item 4 of Amendment No. 1 is incorporated herein by reference. Exhibit 99.5: Form of Voting Agreement, dated February 6, 2025 (incorporated by reference to Exhibit 99.3 of the Issuer's Current Report on Form 8-K filed with the Securities and Exchange Commission on February 6, 2025). AyurMaya Capital Management Company, LP /s/ David E. Goel By: AyurMaya Capital Management Company GP, LLC, General Partner, By: David E. Goel, Managing Member 02/10/2025 David E. Goel /s/ David E. Goel David E. Goel, Individually 02/10/2025