Amendment: SEC Form SC 13G/A filed by Annexon Inc.

 UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

SCHEDULE 13G

(Rule 13d-102)

INFORMATION TO BE INCLUDED IN STATEMENTS FILED PURSUANT

TO RULES 13d-1(b), (c), AND (d) AND AMENDMENTS THERETO FILED

PURSUANT TO RULE 13d-2(b)

(Amendment No. 3)¹

Check the appropriate box to designate the rule pursuant to which this Schedule is filed:

1              The remainder of this cover page shall be filled out for a reporting person’s initial filing on this form with respect to the subject class of securities, and for any subsequent amendment containing information which would alter disclosures provided in a prior cover page.

The information required on the remainder of this cover page shall not be deemed to be “filed” for the purpose of Section 18 of the Securities Exchange Act of 1934 (“Act”) or otherwise subject to the liabilities of that section of the Act but shall be subject to all other provisions of the Act (however, see the Notes).

(1) Includes 1,064,170 Shares (as defined below) underlying certain Pre-funded Warrants (as defined below).

(1) Includes 1,064,170 Shares underlying certain Pre-funded Warrants.

(1) Includes 829,606 Shares underlying certain Pre-funded Warrants.

(1) Includes 829,606 Shares underlying certain Pre-funded Warrants.

(1) Includes 104,244 Shares underlying certain Pre-funded Warrants.

(1) Includes 104,244 Shares underlying certain Pre-funded Warrants.

(1) Includes 1,893,776 Shares underlying certain Pre-funded Warrants.

(1) Includes 2,027,778 Shares underlying certain Pre-funded Warrants.

(1) Includes 2,027,778 Shares underlying certain Pre-funded Warrants.

(1) Includes 2,027,778 Shares underlying certain Pre-funded Warrants.

Annexon, Inc., a Delaware corporation (the “Issuer”).

1400 Sierra Point Parkway, Bldg C, Suite 200

Brisbane, California 94005

Biotechnology Value Fund, L.P. (“BVF”)

44 Montgomery St., 40th Floor

San Francisco, California 94104

Citizenship: Delaware

BVF I GP LLC (“BVF GP”)

44 Montgomery St., 40th Floor

San Francisco, California 94104

Citizenship: Delaware

Biotechnology Value Fund II, L.P. (“BVF2”)

44 Montgomery St., 40th Floor

San Francisco, California 94104

Citizenship: Delaware

BVF II GP LLC (“BVF2 GP”)

44 Montgomery St., 40th Floor

San Francisco, California 94104

Citizenship: Delaware

Biotechnology Value Trading Fund OS LP (“Trading Fund OS”)

PO Box 309 Ugland House

Grand Cayman, KY1-1104

Cayman Islands

Citizenship: Cayman Islands

BVF Partners OS Ltd. (“Partners OS”)

PO Box 309 Ugland House

Grand Cayman, KY1-1104

Cayman Islands

Citizenship: Cayman Islands

BVF GP Holdings LLC (“BVF GPH”)

44 Montgomery St., 40th Floor

San Francisco, California 94104

Citizenship: Delaware

BVF Partners L.P. (“Partners”)

44 Montgomery St., 40th Floor

San Francisco, California 94104

Citizenship: Delaware

BVF Inc.

44 Montgomery St., 40th Floor

San Francisco, California 94104

Citizenship: Delaware

Mark N. Lampert (“Mr. Lampert”)

44 Montgomery St., 40th Floor

San Francisco, California 94104

Citizenship: United States

Each of the foregoing is referred to as a “Reporting Person” and collectively as the “Reporting Persons.”

Common Stock, par value $0.001 per share (the “Shares”).

03589W102

As of the close of business on September 30, 2024, the Reporting Persons and a certain Partners managed account (the “Partners Managed Account”) held certain Pre-funded Warrants (the “Pre-funded Warrants”) exercisable for an aggregate of 2,027,778 Shares. The Pre-funded Warrants are exercisable at any time at an exercise price of $0.001 per Share and do not expire. A holder of Pre-funded Warrants will not be entitled to exercise any such Pre-funded Warrants that, upon giving effect to such exercise, would cause the aggregate number of Shares beneficially owned by such holder (together with its affiliates and any other persons whose beneficial ownership of common stock would be aggregated with the holder for purposes of Section 13(d) of the Exchange Act) to exceed 9.99% of the total number of then issued and outstanding Shares (the “Pre-funded Warrants Blocker). As of the close of business on September 30, 2024, the Pre-funded Warrants Blocker did not limit the exercise of any of the Pre-funded Warrants held by the Reporting Persons and the Partners Managed Account.

As of the close of business on September 30, 2024, (i) BVF beneficially owned 4,757,497 Shares, including 1,064,170 Shares underlying the Pre-funded Warrants held by it, (ii) BVF2 beneficially owned 3,723,121 Shares, including 829,606 Shares underlying the Pre-funded Warrants held by it, and (iii) Trading Fund OS beneficially owned 392,278 Shares, including 104,244 Shares underlying the Pre-funded Warrants held by it.

BVF GP, as the general partner of BVF, may be deemed to beneficially own the 4,757,497 Shares beneficially owned by BVF.

BVF2 GP, as the general partner of BVF2, may be deemed to beneficially own the 3,723,121 Shares beneficially owned by BVF2.

Partners OS, as the general partner of Trading Fund OS, may be deemed to beneficially own the 392,278 Shares beneficially owned by Trading Fund OS.

BVF GPH, as the sole member of each of BVF GP and BVF2 GP, may be deemed to beneficially own the 8,480,618 Shares beneficially owned in the aggregate by BVF and BVF2.

Partners, as the investment manager of BVF, BVF2 and Trading Fund OS, and the sole member of Partners OS, may be deemed to beneficially own the 9,027,778 Shares beneficially owned in the aggregate by BVF, BVF2 and Trading Fund OS and held in the Partners Managed Account, including 154,882 Shares held in the Partners Managed Account, which includes 29,758 Shares underlying the Pre-funded Warrants held in the Partners Managed Account.

BVF Inc., as the general partner of Partners, may be deemed to beneficially own the 9,027,778 Shares beneficially owned by Partners.

Mr. Lampert, as a director and officer of BVF Inc., may be deemed to beneficially own the 9,027,778 Shares beneficially owned by BVF Inc.

The foregoing should not be construed in and of itself as an admission by any Reporting Person as to beneficial ownership of any Shares owned by another Reporting Person. BVF GP disclaims beneficial ownership of the Shares beneficially owned by BVF. BVF2 GP disclaims beneficial ownership of the Shares beneficially owned by BVF2. Partners OS disclaims beneficial ownership of the Shares beneficially owned by Trading Fund OS. BVF GPH disclaims beneficial ownership of the Shares beneficially owned by BVF and BVF2. Each of Partners, BVF Inc. and Mr. Lampert disclaims beneficial ownership of the Shares beneficially owned by BVF, BVF2 and Trading Fund OS and held in the Partners Managed Account, and the filing of this statement shall not be construed as an admission that any such person or entity is the beneficial owner of any such securities.

The following percentages are based upon a denominator that is the sum of (i) 105,653,962 Shares outstanding as of August 8, 2024, as disclosed in the Issuer’s Quarterly Report on Form 10-Q filed with the Securities and Exchange Commission on August 12, 2024, and (ii) certain or all of the 2,027,778 Shares underlying the Pre-funded Warrants held by the Reporting Persons and Partners Managed Account, as applicable.

As of the close of business on September 30, 2024, (i) BVF beneficially owned approximately 4.5% of the outstanding Shares, (ii) BVF2 beneficially owned approximately 3.5% of the outstanding Shares, (iii) Trading Fund OS beneficially owned less than 1% of the outstanding Shares, (iv) BVF GP may be deemed to beneficially own approximately 4.5% of the outstanding Shares, (v) BVF2 GP may be deemed to beneficially own approximately 3.5% of the outstanding Shares, (vi) Partners OS may be deemed to beneficially own less than 1% of the outstanding Shares, (vii) BVF GPH may be deemed to beneficially own approximately 7.9% of the outstanding Shares, and (viii) each of Partners, BVF Inc. and Mr. Lampert may be deemed to beneficially own approximately 8.4% of the outstanding Shares (less than 1% of the outstanding Shares are held in the Partners Managed Account).

See Cover Pages Items 5-9.

See Cover Pages Items 5-9.

See Cover Pages Items 5-9.

See Cover Pages Items 5-9.

Not Applicable.

BVF GPH, Partners, BVF Inc. and Mr. Lampert share voting and dispositive power over the Shares beneficially owned by BVF and BVF2. Partners, BVF Inc. and Mr. Lampert share voting and dispositive power over the Shares beneficially owned by Trading Fund OS and held in the Partners Managed Account.

Not Applicable.

See Exhibit 99.1 to the Schedule 13G filed with the Securities and Exchange Commission on May 26, 2022.

Not Applicable.

By signing below each of the undersigned certifies that, to the best of its knowledge and belief, the securities referred to above were not acquired and are not held for the purpose of or with the effect of changing or influencing the control of the issuer of the securities and were not acquired and are not held in connection with or as a participant in any transaction having that purpose or effect.

SIGNATURE

After reasonable inquiry and to the best of his knowledge and belief, each of the undersigned certifies that the information set forth in this statement is true, complete and correct.

Dated: November 14, 2024