Material Agreement, Financial Obligation, Private Placement (Form 8-K)

Indenture and Notes

On September 12, 2025, Alnylam Pharmaceuticals, Inc. (the "Company") completed its previously announced offering of $575.0 million in aggregate principal amount of 0.00% Convertible Senior Notes due 2028 (the "Initial Notes"). On September 10, 2025, the initial purchasers in such offering exercised their option to purchase an additional $86.25 million in aggregate principal amount of the Company's 0.00% Convertible Senior Notes due 2028 (the "Additional Notes" and together with the Initial Notes, the "Notes"), bringing the total aggregate principal amount of the Notes to $661.25 million. The Notes are the Company's senior unsecured obligations. The Notes were issued pursuant to an Indenture, dated September 12, 2025 (the "Indenture"), between the Company and The Bank of New York Mellon, as trustee. The Indenture includes customary covenants and sets forth certain events of default after which the Notes may be declared immediately due and payable and sets forth certain types of bankruptcy or insolvency events of default involving the Company after which the Notes become automatically due and payable.

The Notes will mature on September 15, 2028, unless earlier converted, redeemed or repurchased. The Notes will not bear regular interest, and the principal amount of the Notes will not accrete. Before June 15, 2028, noteholders will have the right to convert their Notes in certain circumstances and during specified periods. From and after June 15, 2028, the Notes will be convertible at the option of the noteholders at any time prior to the close of business on the second scheduled trading day immediately preceding the maturity date. The Company will settle any conversions of Notes by paying or delivering, as applicable, cash shares of the Company's common stock, par value $0.01 per share (the "Common Stock") or a combination of cash and shares of Common Stock, at the Company's election.

The conversion rate for the Notes will initially be 1.4923 shares of the Common Stock per $1,000 principal amount of Notes, which is equivalent to an initial conversion price of approximately $670.11 per share of the Common Stock. The initial conversion price of the Notes represents a premium of approximately 40.0% above the U.S. composite volume weighted average price of the Common Stock from 12:30 p.m. through 4:00 p.m. Eastern Daylight Time on September 9, 2025, which was $478.6327 per share. The conversion rate is subject to adjustment under certain circumstances in accordance with the terms of the Indenture.

The Company may not redeem the Notes prior to September 20, 2027. The Company may redeem for cash all or any portion of the Notes (subject to certain limitations), at its option, on or after September 20, 2027 and on or prior to the 21st scheduled trading day immediately preceding the maturity date, if the last reported sale price of the Common Stock has been at least 130% of the conversion price then in effect for at least 20 trading days (whether or not consecutive), including the trading day immediately preceding the date on which the Company provides notice of redemption, during any 30 consecutive trading day period ending on, and including, the trading day immediately preceding the date on which the Company provides notice of redemption at a redemption price equal to 100% of the principal amount of the Notes to be redeemed, plus any accrued and unpaid special interest to, but excluding, the redemption date. No sinking fund is provided for the Notes, which means that the Company is not required to redeem or retire the Notes periodically.

Copies of the Indenture and the form of the Notes are attached as Exhibit 4.1 and Exhibit 4.2 hereto, respectively, to this Current Report on Form 8-Kand are incorporated herein by reference. The foregoing description is qualified in its entirety by reference to such exhibits.

Capped Call Transactions

On September 9, 2025, in connection with the pricing of the Initial Notes, the Company entered into privately negotiated capped call transactions (the "Base Capped Call Transactions") with certain initial purchasers of the Notes or their respective affiliates and certain other financial institutions (the "Option Counterparties"). On September 10, 2025, in connection with the initial purchasers' exercise of their option to purchase the Additional Notes, the Company entered into additional privately negotiated capped call transactions with the Option Counterparties (the "Additional Capped Call Transactions," and together with the Base Capped Call Transactions, the "Capped Call Transactions"). The Capped Call Transactions initially cover, subject to customary anti-dilution adjustments, the number of shares of the Common Stock that underlie the Notes. The Capped Call Transactions are expected generally to reduce potential dilution to the Common Stock upon conversion of any Notes and/or offset any potential cash payments the Company is required to make in excess of the principal amount of converted Notes, as the case may be, with such reduction and/or offset subject to a cap. The cap price of the Capped Call Transactions is initially approximately $837.61 per share, which represents a premium of approximately 75.0% above the U.S. composite volume weighted average price of the Common Stock from 12:30 p.m. through 4:00 p.m. Eastern Daylight

Time on September 9, 2025, which was $478.6327 per share, and the cap price is subject to certain adjustments under the terms of the capped call transactions. The Company used approximately $35.3 million of the net proceeds from the offering of Notes to pay the cost of the Capped Call Transactions.

The Capped Call Transactions are separate transactions entered into by the Company with the Option Counterparties, and are not part of the terms of the Notes and will not affect any noteholder's rights under the Notes. Holders of the Notes will not have any rights with respect to the Capped Call Transactions.

The foregoing description of the Capped Call Transactions is qualified in its entirety by the copy of the form of call option transaction confirmation relating to the Capped Call Transactions, which is attached as Exhibit 10.1 hereto and incorporated herein by reference.

The information set forth under Item 1.01 of this Current Report on Form 8-Kis incorporated herein by reference.

The information set forth under Item 1.01 of this Current Report on Form 8-Kis incorporated herein by reference.

The Company offered and sold the Notes to the initial purchasers in reliance on the exemption from registration provided by Section 4(a)(2) of the Securities Act of 1933, as amended (the "Securities Act"), and for resale by the initial purchasers to persons reasonably believed to be qualified institutional buyers pursuant to the exemption from registration provided by Rule 144A under the Securities Act. The Company relied on these exemptions from registration based in part on representations made by the initial purchasers in the purchase agreement pursuant to which the Company sold the Notes to the initial purchasers. The shares of the Common Stock issuable upon conversion of the Notes, if any, have not been registered under the Securities Act and may not be offered or sold in the United States absent registration or an applicable exemption from registration requirements.

To the extent that any shares of the Common Stock are issued upon conversion of the Notes, they will be issued in transactions anticipated to be exempt from registration under the Securities Act by virtue of Section 3(a)(9) thereof, because no commission or other remuneration is expected to be paid in connection with conversion of the Notes and any resulting issuance of shares of the Common Stock. Initially, a maximum of 1,381,483 shares of Common Stock may be issued upon conversion of the Notes, based on the initial maximum conversion rate of 2.0892 shares of Common Stock per $1,000 principal amount of Notes, which is subject to customary anti-dilution adjustment provisions.

Concurrently with the pricing of the Notes, the Company entered into privately negotiated transactions (the "note repurchase transactions") with certain holders of the Company's 1.00% convertible senior notes due 2027 (the "existing notes") to repurchase for cash approximately $637.8 million aggregate principal amount of the existing notes for a total repurchase cost (including accrued and unpaid interest) of approximately $1,105.8 million. The terms of each note repurchase transaction depended on a variety of factors, including the market price of the Common Stock and the trading price of the existing notes at the time of the note repurchase transactions.