[424B5] Bionano Genomics, Inc. Prospectus Supplement (Debt Securities)

Rhea-AI Filing Summary

BNGO updated its at-the-market program to permit sales of common stock of up to $9,924,517 through H.C. Wainwright under a Sales Agreement, subject to General Instruction I.B.6 limits.

For I.B.6 purposes, public float was $47,861,922, based on 9,728,033 non‑affiliate shares on October 9, 2025 and a $4.92 price on September 10, 2025. In the prior 12 months, the company sold $6,029,456 of securities under I.B.6; the new capacity excludes those sales. Wainwright will act as sales agent and receive a 3.0% commission on gross proceeds. The shares trade on Nasdaq as BNGO; the closing price was $1.99 on October 16, 2025.

Filed Pursuant to Rule 424(b)(5)

Registration No. 333-270459

PROSPECTUS SUPPLEMENT

(To Prospectus Supplements Dated April 2, 2025 and February 21, 2025

To Prospectus Dated May 10, 2023)

Up to $9,924,517

Common Stock

This prospectus supplement amends and supplements the information in the prospectus dated May 10, 2023 (the “base prospectus”) and the prospectus supplements, dated April 2, 2025 and February 21, 2025 (collectively, the “ATM Prospectus Supplement” and, together with the base prospectus, the “ATM Prospectus”), filed with the Securities and Exchange Commission, relating to the offer and sale of shares of our common stock, $0.0001 par value per share, from time to time pursuant to the sales agreement dated as of February 21, 2025 (the “Sales Agreement”) with H.C. Wainwright & Co., LLC (“Wainwright”). This prospectus supplement should be read in conjunction with the ATM Prospectus, and is qualified by reference thereto, except to the extent that the information herein amends or supersedes the information contained in the ATM Prospectus. This prospectus supplement is not complete without, and may only be delivered or utilized in connection with, the ATM Prospectus and any future amendments or supplements thereto.

We are filing this prospectus supplement to amend the ATM Prospectus to update the maximum amount of shares that we are eligible to sell under General Instruction I.B.6 of Form S-3 (“General Instruction I.B.6”). As of the date of this prospectus supplement, for purposes of General Instruction I.B.6, the aggregate market value of our outstanding common stock held by non-affiliates, or public float, was $47,861,922, based on 9,728,033 shares of outstanding common stock held by non-affiliates on October 9, 2025, at a price of $4.92 per share, which was the last reported sale price of our common stock on the Nasdaq Capital Market on September 10, 2025, the highest closing sale price of our common stock on the Nasdaq Capital Market within the 60 days prior to the date of this prospectus supplement. During the 12 calendar months prior to and including the date of this prospectus supplement, we have offered and sold aggregate gross proceeds of approximately $6,029,456 of our securities pursuant to General Instruction I.B.6 of Form S-3. Pursuant to General Instruction I.B.6 of Form S-3, and in no event will we sell securities registered on the registration statement of which this prospectus supplement and the ATM Prospectus is a part in a public primary offering with a value exceeding more than one-third of our public float referenced above in any 12-calendar month period so long as our public float remains below $75.0 million.

As a result of these limitations and the current public float of our common stock, and in accordance with the terms of the Sales Agreement, we may offer and sell shares of our common stock having an aggregate offering price of up to $9,924,517 from time to time through Wainwright, which does not include the shares of common stock having an aggregate sales price of approximately $6,029,456 that were sold pursuant to General Instruction I.B.6 of Form S-3 during the 12 calendar months prior to and including the date of this prospectus supplement. In the event that our public float increases above $75.0 million, we will no longer be subject to the limits in General Instruction I.B.6 of Form S-3. If our public float increases such that we may sell additional amounts under the Sales Agreement and the registration statement of which this prospectus supplement and the ATM Prospectus is a part, we will file another prospectus supplement prior to making additional sales.

Our common stock is listed on the Nasdaq Capital Market under the symbol “BNGO.” On October 16, 2025, the closing sale price of our common stock on the Nasdaq Capital Market was $1.99 per share.

Sales of our common stock, if any, under this prospectus supplement and the ATM Prospectus will be made in sales deemed to be “at the market offerings” as defined in Rule 415(a)(4) promulgated under the Securities Act of 1933, as amended (the “Securities Act”). Wainwright is not required to sell any specific amount of securities, but will act as our sales agent using commercially reasonable efforts to sell on our behalf all of the shares of common stock requested to be sold by us, consistent with its normal trading and sales practices, on mutually agreed terms between Wainwright and us. There is no arrangement for funds to be received in any escrow, trust or similar arrangement.

The compensation to Wainwright for sales of common stock sold pursuant to the Sales Agreement will be an amount equal to 3.0% of the gross proceeds of any shares of common stock sold under the Sales Agreement. In connection with the sale of the common stock on our behalf, Wainwright will be deemed to be an “underwriter” within the meaning of the Securities Act and the compensation of Wainwright will be deemed to be underwriting commissions or discounts. We have also agreed to provide indemnification and contribution to Wainwright with respect to certain liabilities, including liabilities under the Securities Act or the Securities Exchange Act of 1934, as amended. See “Plan of Distribution” beginning on page S-13 of the ATM Prospectus Supplement regarding the compensation to be paid to Wainwright.

Investing in our securities involves a high degree of risk. You should review carefully the risks and uncertainties described under the heading “Risk Factors” beginning on page S-6 of the ATM Prospectus Supplement, page 6 of the base prospectus, and under similar headings in the other documents that are incorporated by reference into the ATM Prospectus.

Neither the Securities and Exchange Commission nor any state securities commission has approved or disapproved of these securities or determined if this prospectus supplement is truthful or complete. Any representation to the contrary is a criminal offense.

H.C. Wainwright & Co.

The date of this prospectus supplement is October 17, 2025

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FAQ

What is BNGO offering under this prospectus supplement?

The company may sell shares of common stock of up to $9,924,517 in at-the-market offerings under a Sales Agreement with H.C. Wainwright.

Which rule limits BNGO’s ATM capacity and what is the current public float?

General Instruction I.B.6 of Form S-3 applies. Public float was $47,861,922 based on 9,728,033 non‑affiliate shares on October 9, 2025 using a $4.92 price on September 10, 2025.

How much has BNGO sold under I.B.6 in the last 12 months?

Aggregate gross proceeds of approximately $6,029,456 of its securities.

Who is the sales agent and what is the fee?

H.C. Wainwright & Co., which earns a 3.0% commission on gross proceeds from shares sold under the agreement.

What is BNGO’s Nasdaq symbol and recent closing price?

The symbol is BNGO. The closing price was $1.99 on October 16, 2025.

When would I.B.6 limits no longer apply to BNGO?

If public float increases above $75.0 million, the I.B.6 limits would no longer apply.