Company: DNLI
Filing Date: 2025-02-27
Form Type: S-3ASR
Source: 0001628280-25-008647
Chunk: 15

Company: Denali Therapeutics Inc.
Filing Date: 2025-02-27
Form: S-3ASR
Chunk 15
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, or strategic transactions in, complementary products, technologies or businesses. We do not have agreements or commitments for any specific acquisitions or strategic transactions at this time. 
 See “Use of Proceeds” for more information.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               |
| Risk Factors                                                      |     | Investing in our common stock involves significant risks. See “Risk Factors” for more information.                                                                                                                                                                                                                                                                                                                                                                                                                                                                        |
| Nasdaq symbol                                                     |     | “DNLI”                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |

The number of shares of our common stock to be outstanding after the offering is based on 144,220,986 shares of common stock outstanding as of December 31, 2024, and excludes: • 26,046,065 shares of common stock issuable upon the exercise of pre-funded warrants outstanding as of December 31, 2024; • 18,660,150 shares of common stock issuable upon the exercise of stock options outstanding as of December 31, 2024, at a weighted average exercise price of $25.99 per share; • 4,128,514 shares of common stock issuable upon the vesting of restricted stock units outstanding as of December 31, 2024; • 14,302,049 shares of common stock reserved for future issuance under our 2017 Equity Incentive Plan, or the 2017 Plan, as of December 31, 2024, plus any future increases in the number of shares of common stock reserved for issuance under the 2017 Plan pursuant to the evergreen provision of the 2017 Plan; and • 6,568,147 shares of common stock reserved for future issuance under our 2017 Employee Stock Purchase Plan as of December 31, 2024.

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Except as otherwise indicated, all information in this prospectus supplement assumes:

• no exercise or settlement of stock options, RSUs or other equity awards described above, no exercise of any outstanding warrant, no grant of additional awards under our 2017 Plan, and no issuance of shares under the 2017 Employee Stock Purchase Plan, in each case, after December 31, 2024.

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### RISK FACTORS
Investing in our common stock involves a high degree of risk. Before making a decision to invest in our securities, you should carefully consider the risks and uncertainties described under the heading “Risk Factors” contained or incorporated by reference in this prospectus