ALUMIS INC.

Our named executive officers, including our principal executive officer and the two most highly compensated executive officers, as of December 31, 2025, were:

Summary Compensation Table

The following table presents information concerning the compensation of our named executive officers for the years ended December 31, 2025 and 2024, as applicable:

Narrative to the Summary Compensation Table

Historically, our Board has been responsible for overseeing all aspects of our executive compensation programs. In making compensation determinations, we consider compensation for comparable positions in the market, the historical compensation levels of our executives, individual performance as compared to our expectations and objectives, our desire to motivate our employees to achieve short- and long-term results that are in the best interests of our stockholders and a long-term commitment to our company.

Our Board has historically determined our executive officers’ compensation and has typically reviewed and discussed management’s proposed compensation with our chief executive officer for all executives other than our chief executive officer. Based on those discussions and its discretion, our Board has then approved the compensation of each executive officer.

Annual Base Salary

Base salaries for our executive officers are initially established through arm’s-length negotiations at the time of the executive officer’s hiring, taking into account such named executive officer’s qualifications, experience, the scope of his or her responsibilities and competitive market compensation paid by other companies for similar positions within the industry and geography. Base salaries are reviewed periodically, and adjusted from time to time to realign salaries with market levels after taking into account individual responsibilities, performance and experience.

The 2025 annual base salaries for our named executive officers are set forth in the table below.

2025 Annual Performance Bonus Opportunity

Our executive officers are eligible to earn an annual incentive bonus of up to a percentage of such executive officer’s annual base salary, based on the achievement of pre-established performance objectives determined by the Board.

For 2025, each of Mr. Babler, Dr. Goldstein and Dr. Drappa was eligible to receive a target bonus equal to 55%, 40% and 40% of their base salary, respectively, based on the achievement of certain corporate goals. In January 2026, the Board determined that the 2025 corporate goals were achieved at 140%. As a result, the Board approved annual performance bonuses for Mr. Babler, Dr. Goldstein and Dr. Drappa in the amounts of $524,239, $294,785 and $293,303, respectively, as reported in the “Non-Equity Incentive Plan Compensation” column of the Summary Compensation Table above.

Equity-Based Incentive Awards

Our equity award program is the primary vehicle for offering long-term incentives to our executive officers. We believe that equity awards provide our executives with a strong link to our long-term performance, create an ownership culture and help to align the interests of our executives and our stockholders. To date, we have used stock option grants and RSUs for this purpose because we believe they are an effective means by which to align the long-term interests of our executive officers with those of our stockholders. We believe that our equity awards are an important retention tool for our executive officers, as well as for our other employees. Grants to our executive officers and other employees are made at the discretion of the Board and are not made at any specific time period during a year.

2025 Option Awards

During the fiscal year ended December 31, 2025, we granted options to each of our named executive officers, as shown in more detail in the “Outstanding Equity Awards at Fiscal Year End” table below.

Outstanding Equity Awards at Fiscal Year End

The following table presents the outstanding equity awards held by each named executive officer as of December 31, 2025.

September 15, 2021 vesting commencement date and 1/48th of the shares underlying the option vesting on a monthly basis thereafter, subject to continued service through each vesting date. This option is early exercisable and to the extent any of such shares are unvested as of a given date, any purchased shares will remain subject to a right of repurchase by us upon the termination of the service of the named executive officer. As of December 31, 2025, all shares have vested.

Awards held by our named executive officers may be eligible for accelerated vesting under specified circumstances, as described in more detail below under the subsection titled “—Potential Payments and Benefits upon Termination or Change in Control.”

We may in the future, on an annual basis or otherwise, grant additional equity awards to our executive officers pursuant to our 2024 EIP.

Employment Agreements

Offer Letters

Below are descriptions of our offer letters with our named executive officers. For a discussion of the severance pay and other benefits to be provided in connection with a termination of employment and/or a change in control under the arrangements with our named executive officers, please see the subsection titled “—Potential Payments and Benefits upon Termination or Change in Control.” Each of our named executive officers is employed at will.

Mr. Babler. In September 2021, we and Mr. Babler entered into an offer letter that governs the terms of Mr. Babler’s employment with us. Pursuant to the agreement, Mr. Babler’s employment is at will. Mr. Babler is also entitled to certain severance benefits, the terms of which are described below under the subsection titled “—Potential Payments and Benefits upon Termination or Change in Control.”

Dr. Goldstein. In September 2021, we and Dr. Goldstein entered into an offer letter that governs the terms of Dr. Goldstein’s employment with us. Pursuant to the agreement, Dr. Goldstein’s employment is at will. Dr. Goldstein is also entitled to certain severance benefits, the terms of which are described below under the subsection titled “—Potential Payments and Benefits upon Termination or Change in Control.”

Dr. Drappa. In June 2024, we and Dr. Drappa entered into an offer letter that governs the terms of Dr. Drappa’s employment with us. Pursuant to the agreement, Dr. Drappa’s employment is at will. Dr. Drappa is also entitled to certain severance benefits, the terms of which are described below under the subsection titled “—Potential Payments and Benefits

upon Termination or Change in Control.”

Potential Payments and Benefits upon Termination or Change in Control

Regardless of the manner in which a named executive officer’s service terminates, each named executive officer is entitled to receive unpaid salary earned during his term of service.

Severance and Change in Control Plan

In February 2025, our Compensation Committee adopted our Severance and Change in Control Plan (the “Severance Plan”). The Severance Plan provides for the payment of severance and/or benefits to participants upon a qualifying termination of employment (“Covered Termination”), consisting of either (a) termination of a participant by us without cause (as defined in the Severance Plan) and other than as a result of the participant’s death or disability or (b) the participant’s resignation for good reason (as defined in the Severance Plan).

If a named executive officer experiences a Covered Termination within 12 months following completion of a change in control (as defined in the Severance Plan) (such period, the “Change in Control Period”), such named executive officer shall be eligible to receive the following benefits: (a) a lump sum cash payment equal to 12 months (or in Mr. Babler’s case, 18 months) of base salary (as defined in the Severance Plan); (b) a lump sum cash payment equal to 1.00x to (or in Mr. Babler’s case, 1.50x) the named executive officer’s target bonus (as defined in the Severance Plan) for the calendar year in which the named executive officer’s Covered Termination occurs; (c) COBRA premium payments paid by us for the named executive officer and the named executive officer’s eligible dependents for a period not exceeding the earliest of (1) 12 months (or in Mr. Babler’s case, 18 months) following the date of the named executive officer’s Covered Termination, (2) expiration of the named executive officer’s eligibility for continuation coverage under COBRA, or (3) the date when the named executive officer becomes eligible for a substantially equivalent health insurance coverage in connection with new employment; and (d) full acceleration of any outstanding, unvested equity awards held by the named executive officer.

If a named executive officer experiences a Covered Termination outside of the Change in Control Period, such named executive officer will be eligible to receive (a) cash payments in an amount equal to nine months (or in Mr. Babler’s case, 12 months) of base salary, to be paid in accordance with our regular payroll practices over the length of such period; (b) a pro-rated amount of the named executive officer’s target bonus based upon the number of days worked in the calendar year in which such named executive officer’s Covered Termination occurs, payable in a lump sum no later than the date that all of our other executives would regularly receive the bonus payment; and (c) COBRA premiums paid by us for the named executive officer and named executive officer’s eligible dependents for a period not exceeding nine months (or in Mr. Babler’s case, 12 months).

In addition, as described below, our named executive officers are eligible to receive (a) acceleration of certain outstanding, unvested equity awards granted before the adoption of the Severance Plan pursuant to their offer letters and (b) acceleration of their POP Options (as defined below).

Each named executive officer’s right to receive the payments and benefits provided under the Severance Plan are subject to such named executive officer’s execution, delivery and non-revocation of a separation agreement containing, among other provisions, a general release of all claims in favor us, our subsidiaries and our affiliates.

Offer Letters with Named Executive Officers

Pursuant to each named executive officer’s offer letter, if (a) his employment is terminated without cause (as defined in the offer letter) or (b) in the event of his constructive termination (as defined in the offer letter), then the named executive officer will be entitled to receive acceleration of his then-unvested equity awards that were granted before the adoption of the Severance Plan as to the number of shares underlying such awards that would have been vested as of the first anniversary of the date of his termination, with such acceleration to be effective immediately prior to his termination. These severance benefits are conditioned upon the named executive officer’s delivery of a general release of claims in our favor.

Upon a change of control (as defined in the offer letter) other than an excluded change of control (as defined in the offer letter), 50% of the then-unvested portions of the equity awards that were granted to the named executive officer before the adoption of the Severance Plan will accelerate.

POP Options

Certain benefits apply to the options granted on May 6, 2024, to each of Mr. Babler, Dr. Goldstein and Dr. Drappa, (the “POP Options”) under our 2024 POP. If the officer voluntarily resigns, the POP Options that have satisfied the service condition at the time of termination will remain outstanding and be eligible to vest for one year post-termination if the performance condition(s) with respect to such options are satisfied during the one year post-termination period. If the officer is terminated without cause or by constructive termination (as defined in the 2024 POP), the POP Options that have satisfied the service condition at the time of termination will remain outstanding and be eligible to vest for two years post-termination if the performance condition(s) with respect to such shares are satisfied during the two years post-termination period.

Upon a change in control (as defined in the 2024 POP), with respect to any portion of the performance condition(s) not yet satisfied, if the value of the property expected to be received by our stockholders as a result of such change in control equals or exceeds the applicable share price performance target, a number of shares subject to the POP Options will satisfy the performance condition with respect to such share price performance target as of immediately prior to the change in control.

Additionally, the service condition will be satisfied with respect to 100% of the POP Options immediately prior to a change in control if the officer (i) remains in continuous service through the change in control or (ii) is terminated without cause or by constructive termination prior to a change in control and the change in control occurs within one year following such termination. If the officer is terminated without cause or by constructive termination outside of a change in control, the service-based vesting condition will be satisfied as to an additional 1/3 of shares subject to each of the share price performance targets (see the subsection titled “—Outstanding Equity Awards at Fiscal Year End”).

Pension Benefits

Our named executive officers did not participate in, or otherwise receive any benefits under, any pension or retirement plan sponsored by us during the year ended December 31, 2025.

Nonqualified Deferred Compensation

Our named executive officers did not participate in, or earn any benefits under, a non-qualified deferred compensation plan sponsored by us during the year ended December 31, 2025.

Other Compensation and Benefits

All of our current named executive officers are eligible to participate in our employee benefit plans, in each case on the same basis as all of our other employees. These employee benefit plans include medical, dental, vision, disability, employee assistance, life, accidental death and dismemberment insurance plans. We pay the premiums for the medical, dental, vision, life and accidental death and dismemberment insurance for all of our employees, including our named executive officers. We generally do not provide perquisites or personal benefits to our named executive officers. In addition, we provide the opportunity to participate in a 401(k) plan to our employees, including each of our named executive officers, as discussed in the subsection titled “—401(k) Plan” below.

401(k) Plan

Our named executive officers are eligible to participate in our defined contribution retirement plan that provides eligible employees with an opportunity to save for retirement on a tax advantaged basis. Eligible employees may elect to defer up to 15% of their eligible compensation into the plan on a pretax or after tax basis, up to annual limits prescribed by the Internal Revenue Code of 1986, as amended. Our Board approved a Company match on 100% of each participant’s

employee deferral contributions up to 3% of eligible compensation and a 50% match on each participant’s employee deferral contributions from 3% to 5% of eligible compensation, effective from January 1, 2026.

Compensation Recovery (“Clawback”) Policy

In June 2024, the Board adopted a compensation recovery policy in accordance with the Dodd-Frank Wall Street Reform and Consumer Protection Act and applicable Nasdaq rules, a copy of which was filed as Exhibit 97.1 to our 2024 Annual Report on Form 10-K.

Policies and Practices Related to the Grant of Certain Equity Awards Close in Time to the Release of Material Nonpublic Information

From time to time, we grant stock options to our employees, including our named executive officers. Historically, we have granted new-hire option awards monthly after a new hire’s employment start date and annual refresh employee option grants in the first quarter of each fiscal year, which refresh grants are typically approved by either the Equity Grant Committee described below (except for grants to certain senior employees, including our executive officers) or the Compensation Committee in its regularly scheduled meeting occurring in such quarter. Also, non-employee directors receive automatic grants of initial and annual stock option awards, at the time of a director’s initial appointment or election to the Board, at the time of each annual meeting of our stockholders, and on specifically designated dates for any director who elects to receive some or all of their eligible cash compensation in the form of stock options, pursuant to the Non-Employee Director Compensation Policy, as further described under the heading, “Non-Employee Director Compensation — Non-Employee Director Compensation Policy” below. Other than the delegation by the Board to an Equity Grant Committee of the approval of the issuance of certain equity-based awards to employees and consultants under the 2024 Plan, which awards are typically granted on a monthly basis on the tenth of each month, we do not otherwise maintain any written policies on the timing of awards of stock options, stock appreciation rights, or similar instruments with option-like features. The Compensation Committee considers whether there is any material nonpublic information (“MNPI”) about us when determining the timing of stock option grants and does not seek to time the award of stock options in relation to our public disclosure of MNPI. We havenot timed the release of MNPI for the purpose of affecting the value of executive compensation.

Non-Employee Director Compensation

The following table presents the compensation awarded to or earned by or paid to all individuals who served as non-employee directors during the year ended December 31, 2025. Dr. Colowick and Dr. Tananbaum voluntarily waived all compensation for their service as a director during the year ended December 31, 2025. Mr. Babler, our President and Chief Executive Officer, is also a member of our Board but did not receive any additional compensation for his service as a director. The compensation of Mr. Babler is set forth in the subsection titled “—Summary Compensation Table” above.

The table below presents the aggregate number of shares subject to outstanding stock options, as of December 31, 2025, beneficially owned by each of our non-employee directors for the year ended December 31, 2025.

Non-Employee Director Compensation Policy

In February 2025, our Board adopted an amended and restated non-employee director compensation policy applicable to all of our non-employee directors. In July 2025, the Board amended and restated this policy. The amended and restated policy provides that each such non-employee director will receive the following compensation for service on our Board:

Each of the option grants described above under the non-employee director compensation policy will be granted under our 2024 EIP. Each initial option grant will vest over a three-year period, with 1/36 th of the shares vesting in equal monthly installments following the date of grant, such that the option is fully vested on the third anniversary of the date of grant, subject to the director’s continuous service to us through each such vesting date. The initial grant will vest in full upon a Change in Control (as defined in the 2024 EIP), subject to the director’s continuous service to us through such date. Each annual option grant will vest and become exercisable subject to the director’s continuous service to us through the earlier of the first anniversary of the date of grant or the next annual stockholder meeting. The annual grant will also vest in full upon a Change in Control (as defined in the 2024 EIP), subject to the director’s continuous service to us through such date. The term of each option will be 10 years, subject to earlier termination as provided in the 2024 EIP.

We have reimbursed and will continue to reimburse all of our non-employee directors for their reasonable out-of-pocket expenses incurred in attending board of directors and committee meetings.