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EXHIBIT 10.1

SUMMARY OF CASH COMPENSATION FOR DIRECTORS

     The following cash compensation is paid to members of our board of directors: (1) each of our
non-employee directors receives a fee of $5,000 per fiscal quarter for serving on the board of
directors, (2) each of our directors who serves as the chairman of the board or as the chairman of
the audit committee, compensation committee or nominating and corporate governance committee of the
Board receives an additional $5,000 per year for each such position held; and (3) the chairman of
the audit committee of the board receives an additional $10,000 per year. Directors are reimbursed
for reasonable travel and other expenses incurred in connection with attending meeting of the board
of directors and its committees.exv10w2

 

EXHIBIT 10.2

ALNYLAM PHARMACEUTICALS, INC

2004 STOCK INCENTIVE PLAN, AS AMENDED

1. Purpose

     The purpose of this 2004 Stock Incentive Plan (the “Plan”) of Alnylam Pharmaceuticals,
Inc., a Delaware corporation (the “Company”), is to advance the interests of the Company’s
stockholders by enhancing the Company’s ability to attract, retain and motivate persons who make
(or are expected to make) important contributions to the Company by providing such persons with
equity ownership opportunities and performance-based incentives and thereby better aligning the
interests of such persons with those of the Company’s stockholders. Except where the context
otherwise requires, the term “Company” shall include any of the Company’s present or future parent
or subsidiary corporations as defined in Sections 424(e) or (f) of the Internal Revenue Code of
1986, as amended, and any regulations promulgated thereunder (the “Code”) and any other business
venture (including, without limitation, joint venture or limited liability company) in which the
Company has a controlling interest, as determined by the Board of Directors of the Company (the
“Board”).

2. Eligibility

     All of the Company’s employees, officers, directors, consultants and advisors (including
persons who have entered into an agreement with the Company under which they will be employed by
the Company in the future) are eligible to be granted options or restricted stock awards (each, an
“Award”) under the Plan. Each person who has been granted an Award under the Plan shall be deemed
a “Participant”.

3. Administration and Delegation

     (a) Administration by Board of Directors. The Plan will be administered by the Board.
The Board shall have authority to grant Awards and to adopt, amend and repeal such administrative
rules, guidelines and practices relating to the Plan as it shall deem advisable. The Board may
correct any defect, supply any omission or reconcile any inconsistency in the Plan or any Award in
the manner and to the extent it shall deem expedient to carry the Plan into effect and it shall be
the sole and final judge of such expediency. All decisions by the Board shall be made in the
Board’s sole discretion and shall be final and binding on all persons having or claiming any
interest in the Plan or in any Award. No director or person acting pursuant to the authority
delegated by the Board shall be liable for any action or determination relating to or under the
Plan made in good faith.

     (b) Appointment of Committees. To the extent permitted by applicable law, the Board may
delegate any or all of its powers under the Plan to one or more committees or subcommittees of the
Board (a “Committee”). All references in the Plan to the “Board” shall mean the Board or a
Committee of the Board or the officers referred to in Section 3(c) to the extent that the Board’s
powers or authority under the Plan have been delegated to such Committee or officers.

 

 

     (c)
Delegation to Officers. To the extent permitted by applicable law, the Board may delegate
to one or more officers of the Company the power to grant Awards to employees or officers of the
Company or any of its present or future subsidiary corporations and to exercise such other powers
under the Plan as the Board may determine, provided that the Board shall fix the terms of the
Awards to be granted by such officers (including the exercise price of such Awards, which may
include a formula by which the exercise price will be determined) and the maximum number of shares
subject to Awards that the officers may grant; provided further, however, that no officer shall be
authorized to grant Awards to any “executive officer” of the Company (as defined by Rule 3b-7 under
the Securities Exchange Act of 1934, as amended (the “Exchange Act”)) or to any “officer” of the
Company (as defined by Rule 16a-1 under the Exchange Act).

4. Stock Available for Awards

     (a)
Number of Shares. Subject to adjustment under Section 10, Awards may be made under
the Plan for up to the number of shares of common stock, $0.0001 par value per share, of the
Company (the “Common Stock”) that is equal to the sum of:

          (1)
1,578,947 shares of Common Stock; plus

          (2) such additional number of shares of Common Stock (up to 2,451,315 shares) as is equal to the
sum of (x) the number of shares of Common Stock reserved for issuance under the Company’s 2002 and
2003 Employee, Director and Consultant Stock Plans (the “Existing Plans”) that remain available for
grant under the Existing Plans immediately prior to the closing of the Company’s initial public
offering and (y) the number of shares of Common Stock subject to awards granted under the Existing
Plans which awards expire, terminate or are otherwise surrendered, canceled, forfeited or
repurchased by the Company at their original issuance price pursuant to a contractual repurchase
right (subject, however, in the case of Incentive Stock Options (as hereinafter defined) to any
limitations of the Code); plus

          (3) an annual increase to be added on the first day of each of the Company’s fiscal years during
the period beginning in fiscal year 2005 and ending on the second day of fiscal year 2014 equal to
the lesser of (i) 2,631,578 shares of Common Stock, (ii) five percent (5%) of the outstanding
shares on such date or (iii) an amount determined by the Board.

     Notwithstanding the foregoing, no more than 13,157,894 shares of Common Stock (subject to
adjustment under Section 8) may be issued pursuant to all Awards other than Options (each as
hereinafter defined). Furthermore, notwithstanding clause (3) above, in no event shall the number
of shares available under this Plan be increased as set forth in clause (3) to the extent such
increase, in addition to any other increases proposed by the Board in the number of shares
available for issuance under all other employee or director stock plans, would result in the total
number of shares then available for issuance under all employee and director stock plans exceeding
25% of the outstanding shares of the Company on the first day of the applicable fiscal year.

     If any Award expires or is terminated, surrendered or canceled without having been fully exercised
or is forfeited in whole or in part (including as the result of shares of Common Stock

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subject to
such Award being repurchased by the Company at the original issuance price pursuant to a
contractual repurchase right) or results in any Common Stock not being issued, the unused Common
Stock covered by such Award shall again be available for the grant of Awards under the Plan,
subject, however, in the case of Incentive Stock Options (as hereinafter defined), to any
limitations under the Code. Shares issued under the Plan may consist in whole or in part of
authorized but unissued shares or treasury shares.

     (b) Per-Participant Limit. Subject to adjustment under Section 10, the maximum number of
shares of Common Stock with respect to which Awards may be granted to any Participant under the
Plan shall be 526,315 per calendar year. The per-Participant limit described in this Section 4(b)
shall be construed and applied consistently with Section 162(m) of the Code (“Section 162(m)”).

5. Stock Options

     (a) General. The Board may grant options to purchase Common Stock (each, an “Option”) and
determine the number of shares of Common Stock to be covered by each Option, the exercise price of
each Option and the conditions and limitations applicable to the exercise of each Option, including
conditions relating to applicable federal or state securities laws, as it considers necessary or
advisable. An Option which is not intended to be an Incentive Stock Option (as hereinafter
defined) shall be designated a “Nonstatutory Stock Option”.

     (b) Incentive Stock Options. An Option that the Board intends to be an “incentive stock
option” as defined in Section 422 of the Code (an “Incentive Stock Option”) shall only be granted
to employees of Alnylam Pharmaceuticals, Inc., any of Alnylam Pharmaceuticals, Inc.’s present or
future parent or subsidiary corporations as defined in Sections 424(e) or (f) of the Code, and any
other entities the employees of which are eligible to receive Incentive Stock Options under the
Code, and shall be subject to and shall be construed consistently with the requirements of Section
422 of the Code. The Company shall have no liability to a Participant, or any other party, if an
Option (or any part thereof) that is intended to be an Incentive Stock Option is not an Incentive
Stock Option.

     (c) Exercise Price. The Board shall establish the exercise price at the time each Option is
granted and specify it in the applicable option agreement; provided, however, that the exercise
price shall be not less than 100% of the Fair Market Value (as hereinafter defined) at the time the
Option is granted.

     (d) Duration of Options. Each Option shall be exercisable at such times and subject to such
terms and conditions as the Board may specify in the applicable option agreement; provided,
however, that no Option will be granted for a term in excess of 10 years.

     (e) Exercise of Option. Options may be exercised by delivery to the Company of a written
notice of exercise signed by the proper person or by any other form of notice (including electronic
notice) approved by the Board together with payment in full as specified in Section 5(f) for the
number of shares for which the Option is exercised.

     (f) Payment Upon Exercise. Common Stock purchased upon the exercise of an Option granted under
the Plan shall be paid for as follows:

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          (1) in cash or by check, payable to the order of the Company;

          (2) except as the Board may otherwise provide in an option agreement, by (i) delivery of an
irrevocable and unconditional undertaking by a creditworthy broker to deliver promptly to the
Company sufficient funds to pay the exercise price and any required tax withholding or (ii)
delivery by the Participant to the Company of a copy of irrevocable and unconditional
instructions to a creditworthy broker to pay promptly to the Company the exercise price and any
required tax withholding;

     (3) if provided for in the option agreement or approved by the Company in its sole discretion, by
delivery of shares of Common Stock owned by the Participant valued at their fair market value as
determined by (or in a manner approved by) the Board (“Fair Market Value”), provided (i) such
method of payment is then permitted under applicable law, (ii) such Common Stock, if acquired
directly from the Company, was owned by the Participant at least six months prior to such delivery
and (iii) such Common Stock is not subject to any repurchase, forfeiture, unfulfilled vesting or
other similar requirements; or

     (4) by any combination of the above permitted forms of payment.

     6. Director Options.

     (a) Initial Grant to New Directors. Upon the commencement of service on the Board by any
individual who is not then an employee of the Company or any subsidiary of the Company, the Company
shall grant to such person a Nonstatutory Stock Option to purchase 25,000 shares of Common Stock
(subject to adjustment under Section 8).

     (b) Annual Grant. On the date of each annual meeting of stockholders of the Company, beginning
with the annual meeting in 2005, the Company shall grant a Nonstatutory Stock Option to purchase
10,000 shares of Common Stock (subject to adjustment under Section 8) to each member of the Board
of Directors of the Company (1) who is both serving as a director of the Company immediately prior
to and immediately following such annual meeting, (2) who is not then an employee of the Company or
any of its subsidiaries; and (3) who has served as a director of the Company for at least six
months. In addition, on the date of each annual meeting of stockholders of the Company, beginning
with the annual meeting in 2005, the Company shall grant a Nonstatutory Stock Option to purchase
10,000 shares of Common Stock (subject to adjustment under Section 8) to the Chairman of the Audit
Committee of the Board of Directors of the Company.

     (c) Terms of Director Options. Options granted under this Section 6 shall (i)  have an exercise
price equal to the last reported sale price of the Common Stock on The Nasdaq Stock Market or the
national securities exchange on which the Common Stock is then traded on the date of grant (and if
the Common Stock is not then traded on The Nasdaq Stock Market or a national securities exchange,
the fair market value of the Common Stock on such date as determined by the Board), (ii) expire on
the earlier of 10 years from the date of grant or three months following termination of service as
a director and (iii) contain such other terms and conditions as the Board shall determine. Options
granted under Section 6(a) shall vest as to 8,333 shares on each of the first and second
anniversaries of the date of grant and as to the remaining

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8,334 shares on the third anniversary of
the date of grant subject to the individual’s continued service as a director. Options granted
under Section 6(b) shall vest in full on the first anniversary of the date of grant subject to the
individual’s continued service as a director.

     (d) Board Discretion. The Board retains the specific authority to from time to time increase or
decrease the number of shares subject to Options granted under this Section 6.

7. Restricted Stock

     (a) Grants. The Board may grant Awards entitling recipients to acquire shares of Common
Stock, subject to the right of the Company to repurchase all or part of such shares at their issue
price or other stated or formula price (or to require forfeiture of such shares if issued at no
cost) from the recipient in the event that conditions specified by the Board in the applicable
Award are not satisfied prior to the end of the applicable restriction period or periods
established by the Board for such Award (each, a “Restricted Stock Award”).

     (b) Terms and Conditions. The Board shall determine the terms and conditions of a Restricted
Stock Award, including the conditions for repurchase (or forfeiture) and the issue price, if any.

     (c) Stock Certificates. Any stock certificates issued in respect of a Restricted Stock Award
shall be registered in the name of the Participant and, unless otherwise determined by the Board,
deposited by the Participant, together with a stock power endorsed in blank, with the Company (or
its designee). At the expiration of the applicable restriction periods, the Company (or such
designee) shall deliver the certificates no longer subject to such restrictions to the Participant
or if the Participant has died, to the beneficiary designated, in a manner determined by the Board,
by a Participant to receive amounts due or exercise rights of the Participant in the event of the
Participant’s death (the “Designated Beneficiary”). In the absence of an effective designation by
a Participant, “Designated Beneficiary” shall mean the Participant’s estate.

8. Adjustments for Changes in Common Stock and Certain Other Events

     (a) Changes in Capitalization. In the event of any stock split, reverse stock split,
stock dividend, recapitalization, combination of shares, reclassification of shares, spin-off or
other similar change in capitalization or event, or any distribution to holders of Common Stock
other than an ordinary cash dividend, (i) the number and class of securities available under this
Plan, (ii) the amount of the annual increase in the number of securities available under this Plan
set forth in Section 4(a)(3)(i); (iii) the limit on the number of securities available under this
Plan for Awards other than Options set forth in Section 4(a), (iv) the per-Participant limit set
forth in Section 4(b), (v) the number and class of securities and exercise price per share subject
to each outstanding Option and each Option issuable under Section 6, and (vi) the repurchase price
per share subject to each outstanding Restricted Stock Award, shall be appropriately adjusted by
the Company (or substituted Awards may be made, if applicable) to the extent determined by the
Board.

     (b) Reorganization Events.

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          (1) Definition. A “Reorganization Event” shall mean: (a) any merger or consolidation of the
Company with or into another entity as a result of which all of the Common Stock of the Company is
converted into or exchanged for the right to receive cash, securities or other property, (b) any
exchange of all of the Common Stock of the Company for cash, securities or other property pursuant
to a share exchange transaction or (c) any liquidation or dissolution of the Company.

          (2) Consequences of a Reorganization Event on Awards. In connection with a Reorganization Event,
the Board shall take any one or more of the following actions as to all or any outstanding Awards
on such terms as the Board determines: (i) provide that Awards shall be assumed, or substantially
equivalent Awards shall be substituted, by the acquiring or succeeding corporation (or an affiliate
thereof), (ii) upon written notice to a Participant, provide that the Participant’s unexercised
Options or other unexercised Awards shall become exercisable in full and will terminate immediately
prior to the consummation of such Reorganization Event unless exercised by the Participant within a
specified period following the date of such notice, (iii) in the event of a Reorganization Event
under the terms of which holders of Common Stock will receive upon consummation thereof a cash
payment for each share surrendered in the Reorganization Event (the “Acquisition Price”), make or
provide for a cash payment to a Participant equal to (A) the Acquisition Price times the number of
shares of Common Stock subject to the Participant’s Options or other Awards (to the extent the
exercise price does not exceed the Acquisition Price) minus (B) the aggregate exercise price of all
such outstanding Options or other Awards, in
exchange for the termination of such Options or other Awards, (iv) provide that outstanding
Awards shall become realizable or deliverable, or restrictions applicable to an Award shall lapse,
in whole or in part prior to or upon such Reorganization Event, (v) provide that, in connection
with a liquidation or dissolution of the Company, Awards shall convert into the right to receive
liquidation proceeds (if applicable, net of the exercise price thereof) and (vi) any combination of
the foregoing.

               For purposes of clause (i) above, an Option shall be considered assumed if, following
consummation of the Reorganization Event, the Option confers the right to purchase, for each share
of Common Stock subject to the Option immediately prior to the consummation of the Reorganization
Event, the consideration (whether cash, securities or other property) received as a result of the
Reorganization Event by holders of Common Stock for each share of Common Stock held immediately
prior to the consummation of the Reorganization Event (and if holders were offered a choice of
consideration, the type of consideration chosen by the holders of a majority of the outstanding
shares of Common Stock); provided, however, that if the consideration received as a result of the
Reorganization Event is not solely common stock of the acquiring or succeeding corporation (or an
affiliate thereof), the Company may, with the consent of the acquiring or succeeding corporation,
provide for the consideration to be received upon the exercise of Options to consist solely of
common stock of the acquiring or succeeding corporation (or an affiliate thereof) equivalent in
fair market value to the per share consideration received by holders of outstanding shares of
Common Stock as a result of the Reorganization Event.

               To the extent all or any portion of an Option becomes exercisable solely as a result of clause
(ii) above, the Board may provide that upon exercise of such Option the Participant shall receive
shares subject to a right of repurchase by the Company or its successor

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at the Option exercise
price; such repurchase right (x) shall lapse at the same rate as the Option would have become
exercisable under its terms and (y) shall not apply to any shares subject to the Option that were
exercisable under its terms without regard to clause (ii) above.

               Without limiting the generality of Sections 9(f) and 10(d) below, the Board shall have the
right to amend this Section 8(b)(2) to the extent it deems necessary or advisable.

          (3) Consequences of a Reorganization Event on Restricted Stock Awards. Upon the occurrence of a
Reorganization Event other than a liquidation or dissolution of the Company, the repurchase and
other rights of the Company under each outstanding Restricted Stock Award shall inure to the
benefit of the Company’s successor and shall apply to the cash, securities or other property which
the Common Stock was converted into or exchanged for pursuant to such Reorganization Event in the
same manner and to the same extent as they applied to the Common Stock subject to such Restricted
Stock Award. Upon the occurrence of a Reorganization Event involving the liquidation or
dissolution of the Company, except to the extent specifically provided to the contrary in the
instrument evidencing any Restricted Stock Award or any other agreement between a Participant and
the Company, all restrictions and conditions on all Restricted Stock Awards then outstanding shall
automatically be deemed terminated or satisfied.

9. General Provisions Applicable to Awards

     (a) Transferability of Awards. Except as the Board may otherwise determine or provide in
an Award, Awards shall not be sold, assigned, transferred, pledged or otherwise encumbered by the
person to whom they are granted, either voluntarily or by operation of law, except by will or the
laws of descent and distribution or, other than in the case of an Option intended to be an
Incentive Stock Option, pursuant to a qualified domestic relations order, and, during the life of
the Participant, shall be exercisable only by the Participant. References to a Participant, to the
extent relevant in the context, shall include references to authorized transferees.

     (b) Documentation. Each Award shall be evidenced in such form (written, electronic or
otherwise) as the Board shall determine. Each Award may contain terms and conditions in addition
to those set forth in the Plan.

     (c) Board Discretion. Except as otherwise provided by the Plan, each Award may be made alone
or in addition or in relation to any other Award. The terms of each Award need not be identical,
and the Board need not treat Participants uniformly.

     (d) Termination of Status. The Board shall determine the effect on an Award of the disability,
death, retirement, authorized leave of absence or other change in the employment or other status of
a Participant and the extent to which, and the period during which, the Participant, or the
Participant’s legal representative, conservator, guardian or Designated Beneficiary may exercise
rights under the Award.

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     (e) Withholding. Each Participant shall pay to the Company, or make provision satisfactory to
the Company for payment of, any taxes required by law to be withheld in connection with an Award to
such Participant. Except as the Board may otherwise provide in an Award, for so long as the Common
Stock is registered under the Exchange Act, Participants may satisfy such tax obligations in whole
or in part by delivery of shares of Common Stock, including shares retained from the Award creating
the tax obligation, valued at their Fair Market Value; provided, however, that the total tax
withholding where stock is being used to satisfy such tax obligations cannot exceed the Company’s
minimum statutory withholding obligations (based on minimum statutory withholding rates for federal
and state tax purposes, including payroll taxes, that are applicable to such supplemental taxable
income). Shares surrendered to satisfy tax withholding requirements cannot be subject to any
repurchase, forfeiture, unfulfilled vesting or other similar requirements. The Company may, to the
extent permitted by law, deduct any such tax obligations from any payment of any kind otherwise due
to a Participant.

     (f) Amendment of Award. The Board may amend, modify or terminate any outstanding Award,
including but not limited to, substituting therefor another Award of the same or a different type,
changing the date of exercise or realization, and converting an Incentive Stock Option to a
Nonstatutory Stock Option, provided that the Participant’s consent to such action shall be required
unless the Board determines that the action, taking into account any related action, would not
materially and adversely affect the Participant.

     (g) Conditions on Delivery of Stock. The Company will not be obligated to deliver any shares
of Common Stock pursuant to the Plan or to remove restrictions from shares previously delivered
under the Plan until (i) all conditions of the Award have been met or removed to the satisfaction
of the Company, (ii) in the opinion of the Company’s counsel, all other legal matters in connection
with the issuance and delivery of such shares have been satisfied, including any applicable
securities laws and any applicable stock exchange or stock market rules and regulations, and (iii)
the Participant has executed and delivered to the Company such representations or agreements as the
Company may consider appropriate to satisfy the requirements of any applicable laws, rules or
regulations.

     (h) Acceleration. The Board may at any time provide that any Award shall become immediately
exercisable in full or in part, free of some or all restrictions or conditions, or otherwise
realizable in full or in part, as the case may be.

     (i) Deferrals. The Board may permit Participants to defer receipt of any Common Stock issuable
upon exercise of an Option or upon the lapse of any restriction applicable to any Restricted Stock
Award, subject to such rules and procedures as it may establish.

     (j) Share Issuance. To the extent that the Plan provides for issuance of stock certificates to
reflect the issuance of shares of Common Stock or Restricted Stock, the Board may provide for the
issuance of such shares on a non-certificated basis, to the extent not prohibited by applicable law
or the rules of any stock exchange on which the Common Stock is traded.

10. Miscellaneous

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     (a) No Right To Employment or Other Status. No person shall have any claim or right to be
granted an Award, and the grant of an Award shall not be construed as giving a Participant the
right to continued employment or any other relationship with the Company. The Company expressly
reserves the right at any time to dismiss or otherwise terminate its relationship with a
Participant free from any liability or claim under the Plan, except as expressly provided in the
applicable Award.

     (b) No Rights As Stockholder. Subject to the provisions of the applicable Award, no
Participant or Designated Beneficiary shall have any rights as a stockholder with respect to any
shares of Common Stock to be distributed with respect to an Award until becoming the record holder
of such shares. Notwithstanding the foregoing, in the event the Company effects a split of the
Common Stock by means of a stock dividend and the exercise price of and the number of shares
subject to such Option are adjusted as of the date of the distribution of the dividend (rather than
as of the record date for such dividend), then an optionee who exercises an Option between the
record date and the distribution date for such stock dividend shall be entitled to receive, on the
distribution date, the stock dividend with respect to the shares of Common Stock acquired upon such
Option exercise, notwithstanding the fact that such shares were not outstanding as of the close of
business on the record date for such stock dividend.

     (c) Effective Date and Term of Plan. The Plan shall become effective on the date on which it
is adopted by the Board, but no Award may be granted unless and until the Plan has been approved by
the Company’s stockholders. No Awards shall be granted under the Plan after the completion of 10
years from the earlier of (i) the date on which the Plan was adopted by the Board or (ii) the
date the Plan was approved by the Company’s stockholders, but Awards previously granted may extend
beyond that date.

     (d) Amendment of Plan. The Board may amend, suspend or terminate the Plan or any portion
thereof at any time; provided that, to the extent determined by the Board, no amendment requiring
stockholder approval under any applicable legal, regulatory or listing requirement shall become
effective until such stockholder approval is obtained. No Award shall be made that is conditioned
upon stockholder approval of any amendment to the Plan.

     (e) Provisions for Foreign Participants. The Board may, without amending the Plan, modify
Awards or Options granted to Participants who are foreign nationals or employed outside the United
States or establish subplans under the Plan to recognize differences in laws, rules, regulations or
customs of such foreign jurisdictions with respect to tax, securities, currency, employee benefit
or other matters.

     (f) Governing Law. The provisions of the Plan and all Awards made hereunder shall be governed
by and interpreted in accordance with the laws of the State of Delaware, without regard to any
applicable conflicts of law.

As amended through June 8, 2005

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