Sec Form 4 Filing - Shams Soheil @ Bionano Genomics, Inc - 2021-10-18

FORM 4 Check this box if no longer subject to Section 16. Form 4 or Form 5 obligations may continue. See Instruction 1(b).

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 STATEMENT OF CHANGES IN BENEFICIAL OWNERSHIP Filed pursuant to Section 16(a) of the Securities Exchange Act of 1934, Section 17(a) of the Public Utility Holding Company Act of 1935 or Section 30(h) of the Investment Company Act of 1940

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1. Name and Address of Reporting Person Shams Soheil 2. Issuer Name and Ticker or Trading Symbol Bionano Genomics, Inc [ BNGO] 5. Relationship of Reporting Person(s) to Issuer (Check all applicable) _____ Director _____ 10% Owner X __ Officer (give title below) _____ Other (specify below) Chief Informatics Officer (Last) (First) (Middle) C/O BIONANO GENOMICS, INC., 9540 TOWNE CENTRE DRIVE, SUITE 100 3. Date of Earliest Transaction (MM/DD/YY) 10/18/2021 (Street) SAN DIEGO, CA92121 4. If Amendment, Date Original Filed (MM/DD/YY) 6. Individual or Joint/Group Filing (Check Applicable Line) __ X __ Form filed by One Reporting Person _____ Form filed by More than One Reporting Person (City) (State) (Zip)

Table I - Non-Derivative Securities Acquired, Disposed of, or Beneficially Owned 1.Title of Security (Instr. 3) 2. Transaction Date (MM/DD/YY) 2A. Deemed Execution Date, if any (MM/DD/YY) 3. Transaction Code (Instr. 8) 4. Securities Acquired (A) or Disposed of (D) (Instr. 3, 4 and 5) 5. Amount of Securities Beneficially Owned Following Reported Transaction(s) (Instr. 3 and 4) 6. Ownership Form: Direct (D) or Indirect (I) (Instr. 4) 7. Nature of Indirect Beneficial Ownership (Instr. 4) Code V Amount (A) or (D) Price Common Stock 10/18/2021 A 5,325,378 ( 1 ) A 5,325,378 D

Table II - Derivative Securities Acquired, Disposed of, or Beneficially Owned ( e.g. , puts, calls, warrants, options, convertible securities) 1. Title of Derivative Security (Instr. 3) 2. Conversion or Exercise Price of Derivative Security 3. Transaction Date (MM/DD/YY) 3A. Deemed Execution Date, if any (MM/DD/YY) 4. Transaction Code (Instr. 8) 5. Number of Derivative Securities Acquired (A) or Disposed of (D) (Instr. 3, 4, and 5) 6. Date Exercisable and Expiration Date (MM/DD/YY) 7. Title and Amount of Underlying Securities (Instr. 3 and 4) 8. Price of Derivative Security (Instr. 5) 9. Number of Derivative Securities Beneficially Owned Following Reported Transaction(s) (Instr. 4) 10. Ownership Form of Derivative Security: Direct (D) or Indirect (I) (Instr. 4) 11. Nature of Indirect Beneficial Ownership (Instr. 4) Code V (A) (D) Date Exercisable Expiration Date Title Amount or Number of Shares

Reporting Owners Reporting Owner Name / Address Relationships Director 10% Owner Officer Other Shams Soheil C/O BIONANO GENOMICS, IN C. 9540 TOWNE CENTRE DRIVE, SUITE 100 SAN DIEGO, CA92121 Chief Informatics Officer Signatures /s/ R. Erik Holmlin, Attorney-in-Fact 10/20/2021 Signature of Reporting Person Date

Explanation of Responses:

( 1 )Of which 5,006,479 shares (the "Restricted Shares") are subject to a Stock Restriction Agreement, dated October 8, 2021, by and between the Issuer and Soheil Shams (the Restriction Agreement") and vest as follows: one-third of the Restricted Shares will vest on October 18, 2022 and one-twelfth of the Restricted Shares shall vest every three months following October 18, 2022, in each case subject to Dr. Shams' continuous Service (as defined in the Restriction Agreement). The number of shares that vest upon each vesting date shall be rounded down to the nearest whole share, with the balance of any shares that did not vest as a result of such rounding to vest on the final vesting date, subject to rounding. The unvested shares are subject to adjustment pursuant to the terms of the Merger Agreement (as defined below) and accelerate upon a termination in Service, subject to certain conditions. ( 2 )On October 18, 2021, the Issuer completed its previously announced acquisition (the "Acquisition") of BioDiscovery, Inc. ("BioDiscovery"), as contemplated by that certain Agreement and Plan of Merger, dated as of October 8, 2021 (the "Merger Agreement"), by and among the Issuer, Starship Merger Sub I, Inc., Starship Merger Sub II, LLC, BioDiscovery and Soheil Shams, solely in his capacity as the securityholders' representative. Pursuant to the Acquisition, all outstanding shares of BioDiscovery common stock, no par value, held by Dr. Shams were automatically cancelled and converted into the right to receive (i) cash consideration and (ii) shares of Issuer common stock, $0.0001 par value per share, as specified in the Merger Agreement.

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