EX-4.7



 Exhibit 4.7 

THIS WARRANT AND THE SHARES ISSUABLE HEREUNDER HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED, AND MAY NOT BE SOLD,
PLEDGED, OR OTHERWISE TRANSFERRED WITHOUT AN EFFECTIVE REGISTRATION THEREOF UNDER SUCH ACT OR PURSUANT TO RULE 144 OR AN OPINION OF COUNSEL REASONABLY SATISFACTORY TO THE CORPORATION AND ITS COUNSEL, THAT SUCH REGISTRATION IS NOT REQUIRED. 

WARRANT TO PURCHASE STOCK 

Issuer: BIONANO GENOMICS, INC., a Delaware corporation (the “Company”) 

Number of Shares: 291,667, as the same may be from time to time adjusted pursuant to Article 2 hereof. 

Class of Stock: Series D-1 Convertible Participating Preferred Stock, as the same may be from
time to time adjusted pursuant to Article 2 hereof (the “Shares”) 
 Exercise Price: $0.48 per share, as the same may be from
time to time adjusted pursuant to Article 2 hereof (the “Exercise Price”). 
 Issue Date: December 9, 2016 

Expiration Date: December 9, 2026 

THIS WARRANT CERTIFIES THAT, for the agreed upon value of $1.00 and for other good and valuable consideration, WESTERN ALLIANCE BANK, an
Arizona corporation (“Holder”) is entitled to purchase the number of fully paid and nonassessable Shares of the Company at the Exercise Price per Share set forth, subject to the provisions and upon the terms and conditions set forth in
this Warrant. 
 ARTICLE 1 EXERCISE. 

1.1 Method of Exercise. This Warrant is exercisable, in whole or in part, at any time and from time to time on or before
the Expiration Date set forth above. Holder may exercise this Warrant by delivering this Warrant and a duly executed Notice of Exercise, in substantially the form attached as Appendix 1, to the principal office of Company. Unless Holder is
exercising the conversion right set forth in Section 1.2, Holder shall also deliver to Company a check for the aggregate Exercise Price for Shares being purchased. 

1.2 Conversion Right. In lieu of exercising this Warrant as specified in Section 1.1, Holder may from time to time
convert this Warrant, in whole or in part, into a number of Shares determined by dividing (a) the aggregate fair market value of Shares or other securities otherwise issuable upon exercise of this Warrant minus the aggregate Exercise Price of
such Shares by (b) the fair market value of one Share. The fair market value of Shares shall be determined pursuant to Section 1.3. 

1.3 Fair Market Value. If the Shares are traded in a public market, the fair market value of the Shares shall be the
closing price of the Shares (or the closing price of the Company’s stock into which the Shares are convertible) reported for the business day immediately before Holder delivers its Notice of Exercise to the Company. If the Shares are not traded
in a public market, the Board of Directors of Company shall determine fair market value in its reasonable good faith judgment. The foregoing notwithstanding, if Holder advises the Board of Directors in writing that Holder disagrees with such
determination, then Company and Holder shall promptly agree upon a reputable valuation firm to undertake such valuation. If the valuation determined by such valuation firm is greater than that determined by the Board of Directors, then all fees
and expenses of such valuation firm shall be paid by Company. In all other circumstances, such fees and expenses shall be paid by Holder. 

1.4 Delivery of Certificate and New Warrant. Promptly after Holder exercises or converts this Warrant, Company shall
deliver to a Holder certificate for Shares acquired and, if this Warrant has not been fully exercised or converted and has not expired, a new Warrant representing Shares not so acquired. 

1.5 Replacement of Warrants. On receipt of evidence reasonably satisfactory to Company of the loss, theft, destruction
or mutilation of this Warrant and, in the case of loss, theft or destruction, on delivery of an indemnity agreement reasonably satisfactory in form and amount to Company or, in the case of 

  
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mutilation, on surrender and cancellation of this Warrant, Company at its expense shall execute and deliver, in lieu of this Warrant, a new warrant of like tenor. 

1.6 Repurchase on Sale, Merger, or Consolidation of Company. For the purpose of this Warrant, “Acquisition”
means any sale, license, or other disposition of all or substantially all of the assets of Company, or any reorganization, consolidation, sale of securities or merger of Company where the holders of Company’s securities before the transaction
beneficially own less than 50% of the outstanding voting securities of the surviving entity after the transaction. Upon the closing of any Acquisition, the successor entity shall assume the obligations of this Warrant, and this Warrant shall be
exercisable for the same securities, cash, and property as would be payable for Shares issuable upon exercise of the unexercised portion of this Warrant as if such Shares were outstanding on the record date for the Acquisition and subsequent
closing, and the Exercise Price shall be adjusted accordingly; provided that if pursuant to such Acquisition the entire outstanding class of Shares issuable upon exercise of the unexercised portion of this Warrant are converted into the right
to receive consideration and the total consideration payable to the holders of such class of Shares consists entirely of cash, publicly traded securities or any combination thereof, then, upon payment to the Holder of an amount equal to the
amount such holder would receive if such holder held Shares issuable upon exercise of the unexercised portion of this Warrant and such Shares were outstanding on the record date for the Acquisition less the aggregate Exercise Price of such
Shares, this Warrant shall be cancelled. 
 ARTICLE 2 ADJUSTMENTS. 

2.1 Stock Dividends, Splits, Etc. If Company declares or pays a dividend on its common stock (or Shares if Shares are
securities other than common stock) payable in common stock or other securities or other property, subdivides the outstanding common stock into a greater amount of common stock, or, if Shares are securities other than common stock, subdivides Shares
in a transaction that increases the amount of common stock into which Shares are convertible, then upon exercise of this Warrant, for each Share acquired, Holder shall receive, without cost to Holder, the total number and kind of securities to
which Holder would have been entitled had Holder owned Shares on the record date on which the dividend or subdivision occurred. 

2.2 Reclassification, Recapitalization, Exchange or Substitution. Except in the case of an Acquisition to which
Section 1.6 is applicable, upon any reclassification, recapitalization, exchange, substitution, or other event that results in a change of the number and/or class of the securities issuable upon exercise or conversion of this Warrant, Holder
shall be entitled to receive, upon exercise or conversion of this Warrant, the number and kind of securities and property that Holder would have received for Shares if this Warrant had been exercised immediately before such reclassification,
recapitalization, exchange, substitution, or other event. Company or its successor shall promptly issue to Holder a new Warrant for such new securities or other property. The new Warrant shall provide for adjustments which shall be as nearly
equivalent as may be practicable to the adjustments provided for in this Article 2 including, without limitation, adjustments to the Exercise Price and to the number of securities or property issuable upon exercise of the new Warrant. The provisions
of this Section 2.2 shall similarly apply to successive reclassifications, recapitalizations, exchanges, substitutions, or other events. 

2.3 Adjustments for Combinations, Etc. If the outstanding Shares are combined or consolidated, by reclassification or
otherwise, into a lesser number of shares, the Exercise Price shall be proportionately increased and the number of Shares as to which this Warrant is exercisable shall be proportionately decreased. 

2.4 Adjustments for Diluting Issuances. In the event of the issuance (a “Diluting Issuance”) by Company,
after the Issue Date of this Warrant, of securities at a price per share less than the then Exercise Price, then the number of shares of common stock issuable upon conversion of the Shares, and the conversion price, shall be adjusted in
accordance with those provisions (the “Provisions”) of Company’s Eighth Amended and Restated Certificate of Incorporation (as the same may be amended from time to time, the “Certificate of Incorporation”) which apply to
Diluting Issuances with the same effect as though the shares were outstanding at the time of the diluting issuance. Under no circumstances shall the aggregate Exercise Price payable by Holder upon exercise of this Warrant increase as a result
of any adjustment arising from a Diluting Issuance. 

  
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 2.5 Adjustment for Pay-to-Play Transactions. In the event that the Certificate of Incorporation provides, or is amended to so provide, for the amendment or modification of the rights, preferences or privileges of the
Shares, or the reclassification, conversion or exchange of the outstanding shares of the Class of Stock, in the event that a holder of shares thereof fails to participate in an equity financing transaction (a “Pay-to-Play Provision”), and in the event that such Pay-to-Play Provision becomes operative in a transaction
occurring after the date hereof, this Warrant shall automatically and without any action required become exercisable for that number and type of shares of equity securities as would have been issued or exchanged, or would have remained outstanding,
in respect of the Shares issuable hereunder had this Warrant been exercised in full prior to such event, and had the Holder participated in the equity financing to the maximum extent permitted. 

2.6 No Impairment. Company shall not, by amendment of its Certificate of Incorporation or through a reorganization,
transfer of assets, consolidation, merger, dissolution, issue, or sale of securities or any other voluntary action, avoid or seek to avoid the observance or performance of any of the terms to be observed or performed under this Warrant by Company,
but shall at all times in good faith assist in carrying out of all the provisions of this Article 2 and in taking all such action as may be necessary or appropriate to protect Holder’s rights under this Article against impairment. If Company
takes any dilutive action affecting Shares or its common stock other than as described above that adversely affects Holder’s rights under this Warrant, the Exercise Price shall be adjusted downward and the number of Shares issuable upon
exercise of this Warrant shall be adjusted upward in such a manner that such dilutive action is offset and the aggregate Exercise Price of this Warrant is unchanged. 

2.7 Fractional Shares. No fractional Shares shall be issuable upon exercise or conversion of this Warrant and the
number of Shares to be issued shall be rounded down to the nearest whole Share. If a fractional share interest arises upon any exercise or conversion of this Warrant, Company shall eliminate such fractional share interest by paying Holder an amount
computed by multiplying the fractional interest by the fair market value of a full Share (as determined pursuant to Section 1.6 herein). 

2.8 Certificate as to Adjustments. Upon each adjustment of the Exercise Price, Company at its expense shall promptly
compute such adjustment, and furnish Holder with a certificate of its Chief Financial Officer setting forth such adjustment and the facts upon which such adjustment is based. Company shall, upon written request, furnish Holder a certificate setting
forth the Exercise Price in effect upon the date thereof and the series of adjustments leading to such Exercise Price. 
 ARTICLE 3
COVENANTS OF COMPANY. 
 3.1 Valid Issuance. Company shall take all steps necessary to insure that all Shares which
may be issued upon the exercise of this Warrant, and all securities, if any, issuable upon conversion of Shares, shall, upon issuance, be duly authorized, validly issued, fully paid and nonassessable, and free of any liens and encumbrances except
for restrictions on transfer provided for herein or under applicable federal and state securities laws. 
 3.2 Notice of
Certain Events. If Company proposes at any time (a) to declare any dividend or distribution upon its common stock, whether in cash, property, stock, or other securities and whether or not a regular cash dividend; (b) to offer for
subscription pro rata to the holders of any class or series of its stock any additional shares of stock of any class or series or other rights; (c) to effect any reclassification or recapitalization of common stock; (d) to effect an
Acquisition; or (e) offer holders of registration rights the opportunity to participate in an underwritten public offering of the company’s securities for cash, then, in connection with each such event, Company shall give Holder
(1) in the case of the matters referred to in (a) and (b) above at least 20 days prior written notice of the date on which a record will be taken for such dividend, distribution, or subscription rights (and specifying the date on
which the holders of common stock will be entitled thereto) or for determining rights to vote, if any, in respect of the matters referred to in (c) and (d) above; (2) in the case of the matters referred to in (c) and (d) above at
least 20 days prior written notice of the date when the same will take place (and specifying the date on which the holders of common stock will be entitled to exchange their common stock for securities or other property deliverable upon the
occurrence of such event); and (3) in the case of the matter referred to in (e) above, the same notice as is given to the holders of such registration rights. 

  
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 3.3 Information. So long as the Holder holds this Warrant and/or any of
the Shares, Company shall deliver to Holder (a) promptly, copies of all notices or other written communications to which Holder would be entitled if it held Shares as to which this Warrant was then exercisable and (b) such other financial
statements required under and in accordance with any loan documents between Holder and Company, or if there are no such requirements or if the subject loan(s) are no longer are outstanding, then within 90 days after the end of each of the first
three quarters of each fiscal year, Company’s quarterly, unaudited financial statements and within 180 days after the end of each fiscal year, Company’s annual, audited financial statements. 

3.4 Notice of Expiration. Company shall give Holder written notice of Holder’s right to exercise this Warrant in
the form attached as Appendix 2 not more than 90 days and not less than 15 days before the Expiration Date and, in the case of an Acquisition to which the proviso of Section 1.6 shall be applicable, 15 days before such Acquisition. If the
notice is not so given, the Expiration Date shall automatically be extended until 15 days after the date Company delivers the notice to Holder. 

3.5 Registration Rights. The common stock issuable upon conversion of Shares, shall have the same “piggyback”
registration rights as are set forth in the Fifth Amended and Restated Investors’ Rights Agreement, dated as of August 5, 2016 between Company and its investors, as from time to time in effect (the “Investors’ Rights
Agreement” — a true copy of which as in effect on the date hereof has been furnished by Company to Holder) and by accepting this Warrant, Holder agrees to be subject to corresponding obligations of the holders of “piggyback”
registration rights. Company agrees that no amendments will be made to the Investors’ Rights Agreement which would have an adverse impact on Holder’s registration rights thereunder. 

ARTICLE 4 MISCELLANEOUS. 

4.1 Legends. This Warrant and the Shares (and the securities issuable, directly or indirectly, upon conversion of
Shares, if any) shall be imprinted with a legend in substantially the following form: 
 THIS SECURITY HAS NOT BEEN REGISTERED UNDER THE
SECURITIES ACT OF 1933, AS AMENDED, AND MAY NOT BE SOLD, PLEDGED OR OTHERWISE TRANSFERRED WITHOUT AN EFFECTIVE REGISTRATION THEREOF UNDER SUCH ACT OR PURSUANT TO RULE 144 OR AN OPINION OF COUNSEL REASONABLY SATISFACTORY TO COMPANY AND ITS COUNSEL
THAT SUCH REGISTRATION IS NOT REQUIRED. 
 4.2 Compliance with Securities Laws on Transfer. This Warrant and the
Shares issuable upon exercise of this Warrant (and the securities issuable, directly or indirectly, upon conversion of Shares, if any) may not be transferred or assigned in whole or in part without compliance with applicable federal and state
securities laws by the transferor and the transferee (including, without limitation, the delivery of investment representation letters and legal opinions reasonably satisfactory to Company, as reasonably requested by Company). Company shall not
require Holder to provide an opinion of counsel if the transfer is to Holder’s parent company, Western Alliance Bancorporation, or any other affiliate or successor of Holder, or if there is no material question as to the availability of current
information as referenced in Rule 144(c), Holder represents that it has complied with Rule 144(d) and (e) in reasonable detail, the selling broker represents that it has complied with Rule 144(f), and the Company is provided with a copy of
Holder’s notice of proposed sale. 
 4.3 Transfer Procedure. After receipt by Holder of the executed Warrant,
Holder will transfer all of this Warrant to Holder’s parent company, Western Alliance Bancorporation, by execution of an Assignment substantially in the form of Appendix 3. Subject to the provisions of Section 4.2 above and upon providing
Company with written notice, Western Alliance Bancorporation and any subsequent Holder may transfer all or part of this Warrant or the Shares issuable upon exercise of this Warrant (or the Shares issuable directly or indirectly, upon conversion of
the Shares, if any) to any transferee, provided, however, in connection with any such transfer, Western Alliance Bancorporation or any subsequent Holder will give the Company notice of the portion of this Warrant being transferred with the name,
address and taxpayer identification number of the transferee and Holder will surrender this Warrant to the Company for reissuance to the transferee(s) (and Holder if applicable). Unless Company is filing financial information with the SEC pursuant
to the Securities Exchange Act of 1934, Company shall have the right to refuse to transfer any portion of this Warrant to any person who directly or indirectly competes with Company. 

  
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 4.4 Notices. All notices and other communications from Company to Holder,
or vice versa, shall be in writing and shall be deemed delivered and effective when given personally or mailed by first-class registered or certified mail, postage prepaid, or by overnight courier, at such address as may have been furnished to
Company or Holder, as the case may be, in writing by Company or such Holder from time to time. 
 4.5 Attorneys Fees.
In the event of any dispute between the parties concerning the terms and provisions of this Warrant, the party prevailing in such dispute shall be entitled to collect from the other party all costs incurred in such dispute, including reasonable
attorneys’ fees. 
 4.6 Governing Law. This Warrant shall be governed by and construed in accordance with the
laws of the State of California, without giving effect to its principles regarding conflicts of law. 
 4.7 Market Stand-Off Agreement. Holder hereby agrees that it shall not sell, dispose of, transfer, make any short sale of, grant any option for the purchase of, or enter into any hedging or similar transaction with
the same economic effect as a sale, any shares of the Company’s Common Stock or other securities held by such Holder (other than those included in the registration) during (i) the 180-day period
following the effective date of the Company’s first underwritten public offering of its Common Stock registered under the Securities Act of 1933, as amended (the “Securities Act”) (or such longer period as the underwriters or the
Company shall request in order to facilitate compliance with NASD Rule 2711 or NYSE Member Rule 472 or any successor or similar rule or regulation), and (ii) the 90-day period following the effective date
of a registration statement of the Company filed under the Securities Act (or such longer period as the underwriters or the Company shall request in order to facilitate compliance with NASD Rule 2711 or NYSE Member Rule 472 or any successor or
similar rule or regulation); provided, that, with respect to (i) and (ii) above, all officers and directors of the Company are bound by and have entered into similar agreements. The underwriters of the Company’s stock are intended third
party beneficiaries of this Section 4.7 and shall have the right, power and authority to enforce the provisions hereof as though they were a party hereto. 

[Balance of Page Intentionally Left Blank] 

  
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 IN WITNESS WHEREOF, Company has caused this Warrant to be duly executed by its
authorized officers, all as of the day and year first above written. 
  

			
	COMPANY
	
	BIONANO GENOMICS, INC.
		
	By:	 	/s/ R. Erik Holmlin
	Name:	 	R. Erik Holmlin
	Title:	 	CEO









 APPENDIX 1 

Notice of Exercise 
 [Strike
paragraph that does not apply.] 
 1. The undersigned hereby elects to purchase
             shares of the Common/Series              Preferred [strike one] Stock of BIONANO GENOMICS, INC.
pursuant to the terms of the attached Warrant, and tenders herewith payment of the purchase price of such shares in full. 
 1. The
undersigned hereby elects to convert the attached Warrant into Shares/cash [strike one] in the manner specified in the Warrant. This conversion is exercised with respect to
                             of the Shares covered by the Warrant. 

2. Please issue a certificate or certificates representing said shares in the name of the undersigned or in such other name as is specified
below: 
  

					
	 Name:
	  	 	  	
	 Address:
	  	 	  	
	 	  	

 3. The undersigned represents it is acquiring the shares solely for its own account and not as a nominee for
any other party and not with a view toward the resale or distribution thereof except in compliance with applicable securities laws. 
  

	
	(Signature)
	
	   

	(Date)



  
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 APPENDIX 2 

Notice that Warrant Is About to Expire 

[Insert Date of Notice] 
  

	To:	 BRIDGE BANK, A DIVISION OF WESTERN ALLIANCE BANK 



Attn:                    
     
 55 Almaden Boulevard 

San Jose, California 95113 

The Warrant issued to you described below will expire on
                    ,         . 

 

			
	 Issuer:
	  	 BIONANO GENOMICS, INC.

		
	 Issue Date:
	  	 December 9, 2016

		
	 Class of Security Issuable:
	  	
                   
     

		
	 Exercise Price per Share:
	  	 $             per
share

		
	 Number of Shares Issuable:
	  	
                   
     


 Procedure for Exercise: 

Please contact                     
at (        )         -         with any questions you may have concerning exercise of the Warrant. This is
your only notice of pending expiration. 
  

			
	BIONANO GENOMICS, INC.


 
			
		
	By	 	 


 
			
	Its:	 	 



  
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 APPENDIX 3 

Assignment 
 For value received,
WESTERN ALLIANCE BANK, an Arizona corporation hereby sells, assigns and transfers unto: 
  

					
		 	 Name:
	  	WESTERN ALLIANCE BANCORPORATION
		 	 Address:
	  	 55 Almaden Boulevard
 San Jose, California
95113

		 	 Tax I D:
	  	                    

 that certain Warrant to Purchase Stock issued by BIONANO GENOMICS, INC. (the “Company”), on
December 9, 2016 (the “Warrant”) together with all rights, title and interest therein. 
  

			
	 WESTERN ALLIANCE BANK, AN ARIZONA
CORPORATION



 
			
		
	 By:
	 	 
	 Name:  
	 	 
	 Title:
	 	 



Date:                      
    
 By its execution below, and for the benefit of the Company, Western Alliance Bancorporation agrees to all provisions of
the Warrant as of the date hereof. 
  

			
	 WESTERN ALLIANCE BANCORPORATION





			
		
	 By:
	 	 
	 Name:  
	 	 
	 Title:
	 	 



  
 1