0001847367--12-31Q30000000000http://fasb.org/us-gaap/2025#UsefulLifeShorterOfTermOfLeaseOrAssetUtilityMember47222419971742310.2139http://fasb.org/us-gaap/2025#DerivativeGainLossOnDerivativeNethttp://fasb.org/us-gaap/2025#UsefulLifeShorterOfTermOfLeaseOrAssetUtilityMember0.10.00010.0001false0001847367us-gaap:AdditionalPaidInCapitalMemberus-gaap:PrivatePlacementMember2024-07-012024-09-300001847367us-gaap:AdditionalPaidInCapitalMemberus-gaap:IPOMember2024-07-012024-09-300001847367us-gaap:PrivatePlacementMember2024-07-012024-09-300001847367us-gaap:CommonStockMember2024-04-012024-06-300001847367us-gaap:CommonStockMember2024-01-012024-03-310001847367us-gaap:CommonStockMember2025-07-012025-09-300001847367us-gaap:CommonStockMemberus-gaap:PrivatePlacementMember2024-07-012024-09-300001847367us-gaap:CommonStockMemberus-gaap:IPOMember2024-07-012024-09-300001847367us-gaap:RetainedEarningsMember2025-09-300001847367us-gaap:AdditionalPaidInCapitalMember2025-09-300001847367us-gaap:AccumulatedOtherComprehensiveIncomeMember2025-09-300001847367us-gaap:RetainedEarningsMember2025-06-300001847367us-gaap:AdditionalPaidInCapitalMember2025-06-300001847367us-gaap:AccumulatedOtherComprehensiveIncomeMember2025-06-3000018473672025-06-300001847367us-gaap:RetainedEarningsMember2025-03-310001847367us-gaap:AdditionalPaidInCapitalMember2025-03-310001847367us-gaap:AccumulatedOtherComprehensiveIncomeMember2025-03-3100018473672025-03-310001847367us-gaap:RetainedEarningsMember2024-12-310001847367us-gaap:AdditionalPaidInCapitalMember2024-12-310001847367us-gaap:AccumulatedOtherComprehensiveIncomeMember2024-12-310001847367us-gaap:RetainedEarningsMember2024-09-300001847367us-gaap:AdditionalPaidInCapitalMember2024-09-300001847367us-gaap:AccumulatedOtherComprehensiveIncomeMember2024-09-300001847367us-gaap:RetainedEarningsMember2024-06-300001847367us-gaap:AdditionalPaidInCapitalMember2024-06-300001847367us-gaap:AccumulatedOtherComprehensiveIncomeMember2024-06-3000018473672024-06-300001847367us-gaap:RetainedEarningsMember2024-03-310001847367us-gaap:AdditionalPaidInCapitalMember2024-03-310001847367us-gaap:AccumulatedOtherComprehensiveIncomeMember2024-03-310001847367us-gaap:RetainedEarningsMember2023-12-310001847367us-gaap:AdditionalPaidInCapitalMember2023-12-310001847367us-gaap:AccumulatedOtherComprehensiveIncomeMember2023-12-310001847367us-gaap:IPOMember2024-07-010001847367alms:SeriesCRedeemableConvertiblePreferredStockMember2024-03-310001847367alms:SeriesC1RedeemableConvertiblePreferredStockMember2024-03-310001847367us-gaap:RestrictedStockMemberus-gaap:ShareBasedPaymentArrangementNonemployeeMember2021-02-280001847367alms:EarlyExercisableEmployeeStockOptionsMember2025-01-012025-09-300001847367alms:StockOptionPlansExcludingPerformanceOptionPlan2024Member2024-01-012024-09-300001847367alms:StockOptionPlansExcludingPerformanceOptionPlan2024Member2024-01-012024-12-310001847367alms:PerformanceOptionPlan2024Member2024-01-012024-12-310001847367alms:PerformanceOptionPlan2024Member2025-09-300001847367alms:PerformanceOptionPlan2024Member2024-12-3100018473672024-03-290001847367alms:StockOptionPlansExcludingPerformanceOptionPlan2024Member2024-12-310001847367alms:NonPerformancePlansMember2025-01-012025-09-300001847367alms:NonPerformancePlansMember2024-01-012024-09-300001847367alms:StockOptionPlansExcludingPerformanceOptionPlan2024Member2025-09-300001847367alms:TwoThousandTwentyOneStockPlanMember2024-06-300001847367srt:MinimumMemberus-gaap:EmployeeStockOptionMemberalms:NonPerformancePlansMember2025-01-012025-09-300001847367srt:MaximumMemberus-gaap:EmployeeStockOptionMemberalms:NonPerformancePlansMember2025-01-012025-09-300001847367srt:MinimumMemberalms:EmployeeStockPurchasePlan2024Member2025-01-012025-09-300001847367srt:MaximumMemberalms:EmployeeStockPurchasePlan2024Member2025-01-012025-09-300001847367alms:PerformanceOptionPlan2024Member2024-05-012024-05-310001847367srt:MinimumMemberus-gaap:EmployeeStockOptionMemberalms:NonPerformancePlansMember2024-01-012024-09-300001847367srt:MaximumMemberus-gaap:EmployeeStockOptionMemberalms:NonPerformancePlansMember2024-01-012024-09-300001847367us-gaap:EmployeeStockOptionMemberalms:NonPerformancePlansMember2025-01-012025-09-300001847367alms:EmployeeStockPurchasePlan2024Member2025-01-012025-09-300001847367us-gaap:EmployeeStockOptionMemberalms:NonPerformancePlansMember2024-01-012024-09-300001847367us-gaap:RestrictedStockUnitsRSUMember2025-09-300001847367us-gaap:RestrictedStockMember2024-12-310001847367alms:AcelyrinIncMemberus-gaap:EmployeeSeveranceMember2025-01-012025-12-310001847367alms:AcelyrinIncMemberus-gaap:ResearchAndDevelopmentExpenseMemberus-gaap:EmployeeSeveranceMember2025-07-012025-09-300001847367alms:AcelyrinIncMemberus-gaap:GeneralAndAdministrativeExpenseMemberus-gaap:EmployeeSeveranceMember2025-07-012025-09-300001847367alms:AcelyrinIncMemberus-gaap:EmployeeSeveranceMember2025-07-012025-09-300001847367alms:AcelyrinIncMemberus-gaap:ResearchAndDevelopmentExpenseMemberus-gaap:EmployeeSeveranceMember2025-01-012025-09-300001847367alms:AcelyrinIncMemberus-gaap:GeneralAndAdministrativeExpenseMemberus-gaap:EmployeeSeveranceMember2025-01-012025-09-300001847367alms:AcelyrinIncMemberus-gaap:EmployeeSeveranceMember2025-01-012025-09-300001847367alms:MaterialRightObligationMemberalms:KakenPharmaceuticalCo.LtdMemberalms:CollaborativeArrangementForProductEsk001Member2025-09-300001847367alms:DevelopmentServicesObligationMemberalms:KakenPharmaceuticalCo.LtdMemberalms:CollaborativeArrangementForProductEsk001Member2025-09-300001847367alms:LicenseObligationMemberalms:KakenPharmaceuticalCo.LtdMemberalms:CollaborativeArrangementForProductEsk001Member2025-07-012025-09-300001847367alms:DevelopmentServicesObligationAndManufacturingServicesObligationMemberalms:KakenPharmaceuticalCo.LtdMemberalms:CollaborativeArrangementForProductEsk001Member2025-07-012025-09-300001847367alms:CollaborationRevenueMemberalms:SingleReportableSegmentMember2025-07-012025-09-300001847367alms:CollaborationRevenueMember2025-07-012025-09-300001847367alms:LicenseObligationMemberalms:KakenPharmaceuticalCo.LtdMemberalms:CollaborativeArrangementForProductEsk001Member2025-01-012025-09-300001847367alms:DevelopmentServicesObligationAndManufacturingServicesObligationMemberalms:KakenPharmaceuticalCo.LtdMemberalms:CollaborativeArrangementForProductEsk001Member2025-01-012025-09-300001847367us-gaap:LicenseMemberalms:SingleReportableSegmentMember2025-01-012025-09-300001847367alms:CollaborationRevenueMemberalms:SingleReportableSegmentMember2025-01-012025-09-300001847367us-gaap:LicenseMember2025-01-012025-09-300001847367alms:CollaborationRevenueMember2025-01-012025-09-300001847367alms:AcelyrinIncMemberus-gaap:EmployeeSeveranceMember2025-09-300001847367alms:AssetPledgedAsCollateralForLeaseCommitmentsMember2025-09-300001847367alms:AssetPledgedAsCollateralForLeaseCommitmentsMember2024-12-310001847367alms:ForesiteLabsMemberus-gaap:RelatedPartyMember2025-07-012025-09-300001847367us-gaap:RelatedPartyMember2025-07-012025-09-300001847367us-gaap:RelatedPartyMember2025-01-012025-09-300001847367alms:ForesiteLabsMemberus-gaap:RelatedPartyMember2024-07-012024-09-300001847367us-gaap:RelatedPartyMember2024-07-012024-09-300001847367alms:ForesiteLabsMemberus-gaap:RelatedPartyMember2024-01-012024-09-300001847367us-gaap:RelatedPartyMember2024-01-012024-09-300001847367us-gaap:SoftwareDevelopmentMember2025-09-300001847367us-gaap:LeaseholdImprovementsMember2025-09-300001847367us-gaap:FurnitureAndFixturesMember2025-09-300001847367us-gaap:ComputerEquipmentMember2025-09-300001847367alms:LaboratoryEquipmentMember2025-09-300001847367us-gaap:SoftwareDevelopmentMember2024-12-310001847367us-gaap:LeaseholdImprovementsMember2024-12-310001847367us-gaap:FurnitureAndFixturesMember2024-12-310001847367us-gaap:ComputerEquipmentMember2024-12-310001847367alms:LaboratoryEquipmentMember2024-12-3100018473672024-07-010001847367us-gaap:AccumulatedOtherComprehensiveIncomeMember2025-07-012025-09-300001847367us-gaap:AccumulatedOtherComprehensiveIncomeMember2025-04-012025-06-300001847367us-gaap:AccumulatedOtherComprehensiveIncomeMember2025-01-012025-03-310001847367us-gaap:AccumulatedOtherComprehensiveIncomeMember2024-07-012024-09-300001847367us-gaap:AccumulatedOtherComprehensiveIncomeMember2024-01-012024-03-310001847367us-gaap:RetainedEarningsMember2025-07-012025-09-300001847367us-gaap:RetainedEarningsMember2025-04-012025-06-300001847367us-gaap:RetainedEarningsMember2025-01-012025-03-310001847367us-gaap:RetainedEarningsMember2024-07-012024-09-300001847367us-gaap:RetainedEarningsMember2024-04-012024-06-300001847367us-gaap:RetainedEarningsMember2024-01-012024-03-3100018473672025-01-3100018473672024-12-012024-12-310001847367us-gaap:FairValueInputsLevel2Memberus-gaap:FairValueMeasurementsRecurringMemberus-gaap:USTreasurySecuritiesMember2025-09-300001847367us-gaap:FairValueInputsLevel2Memberus-gaap:FairValueMeasurementsRecurringMemberus-gaap:CorporateDebtSecuritiesMember2025-09-300001847367us-gaap:FairValueInputsLevel2Memberus-gaap:FairValueMeasurementsRecurringMemberus-gaap:CommercialPaperMember2025-09-300001847367us-gaap:FairValueInputsLevel2Memberus-gaap:FairValueMeasurementsRecurringMemberalms:SupranationalDebtObligationsMember2025-09-300001847367us-gaap:FairValueInputsLevel2Memberus-gaap:FairValueMeasurementsRecurringMemberalms:GovernmentDevelopmentBankObligationsMember2025-09-300001847367us-gaap:FairValueInputsLevel1Memberus-gaap:FairValueMeasurementsRecurringMemberus-gaap:USTreasurySecuritiesMember2025-09-300001847367us-gaap:FairValueMeasurementsRecurringMemberus-gaap:USTreasurySecuritiesMember2025-09-300001847367us-gaap:FairValueMeasurementsRecurringMemberus-gaap:CorporateDebtSecuritiesMember2025-09-300001847367us-gaap:FairValueMeasurementsRecurringMemberus-gaap:CommercialPaperMember2025-09-300001847367us-gaap:FairValueMeasurementsRecurringMemberalms:SupranationalDebtObligationsMember2025-09-300001847367us-gaap:FairValueMeasurementsRecurringMemberalms:GovernmentDevelopmentBankObligationsMember2025-09-300001847367us-gaap:FairValueInputsLevel2Memberus-gaap:FairValueMeasurementsRecurringMemberus-gaap:USTreasurySecuritiesMember2024-12-310001847367us-gaap:FairValueInputsLevel1Memberus-gaap:FairValueMeasurementsRecurringMemberus-gaap:USTreasurySecuritiesMember2024-12-310001847367us-gaap:FairValueMeasurementsRecurringMemberus-gaap:USTreasurySecuritiesMember2024-12-310001847367srt:MinimumMemberus-gaap:MeasurementInputRiskFreeInterestRateMember2024-09-300001847367srt:MinimumMemberus-gaap:MeasurementInputPriceVolatilityMember2024-09-300001847367srt:MinimumMemberus-gaap:MeasurementInputExpectedTermMember2024-09-300001847367srt:MinimumMemberalms:MeasurementInputProbabilityOfOccurrenceMember2024-09-300001847367srt:MaximumMemberus-gaap:MeasurementInputRiskFreeInterestRateMember2024-09-300001847367srt:MaximumMemberus-gaap:MeasurementInputPriceVolatilityMember2024-09-300001847367srt:MaximumMemberus-gaap:MeasurementInputExpectedTermMember2024-09-300001847367srt:MaximumMemberalms:MeasurementInputProbabilityOfOccurrenceMember2024-09-300001847367us-gaap:MeasurementInputExpectedDividendRateMember2024-09-300001847367alms:VotingCommonStockMember2024-03-310001847367alms:KakenPharmaceuticalCo.LtdMemberalms:CollaborativeArrangementForProductEsk001Member2025-09-300001847367us-gaap:CommonStockMember2025-09-300001847367us-gaap:CommonStockMember2025-06-300001847367us-gaap:CommonStockMember2025-03-310001847367us-gaap:CommonStockMember2024-12-310001847367us-gaap:CommonStockMember2024-09-300001847367us-gaap:CommonStockMember2024-06-300001847367us-gaap:CommonStockMember2024-03-310001847367us-gaap:CommonStockMember2023-12-310001847367us-gaap:NonvotingCommonStockMember2025-09-300001847367us-gaap:NonvotingCommonStockMember2024-12-310001847367alms:VotingCommonStockMember2024-12-310001847367alms:SharesAvailableForGrantUnderShareBasedPaymentPlansMemberalms:TwoThousandTwentyFourPerformanceOptionPlanMember2025-09-300001847367alms:SharesAvailableForGrantUnderShareBasedPaymentPlansMemberalms:TwoThousandTwentyFourEquityIncentivePlanMember2025-09-300001847367alms:SharesAvailableForGrantUnderShareBasedPaymentPlansMemberalms:TwoThousandTwentyFourEmployeeStockPurchasePlanMember2025-09-300001847367alms:SharesAvailableForGrantUnderShareBasedPaymentPlansMemberalms:Acelyrin2023EquityIncentivePlanMember2025-09-300001847367us-gaap:RestrictedStockUnitsRSUMember2025-09-300001847367us-gaap:EmployeeStockOptionMember2025-09-300001847367alms:AcelyrinIncMemberalms:AcelyrinPlansMember2025-05-210001847367alms:SharesAvailableForGrantUnderShareBasedPaymentPlansMemberalms:TwoThousandTwentyFourPerformanceOptionPlanMember2024-12-310001847367alms:SharesAvailableForGrantUnderShareBasedPaymentPlansMemberalms:TwoThousandTwentyFourEquityIncentivePlanMember2024-12-310001847367alms:SharesAvailableForGrantUnderShareBasedPaymentPlansMemberalms:TwoThousandTwentyFourEmployeeStockPurchasePlanMember2024-12-310001847367us-gaap:EmployeeStockOptionMember2024-12-310001847367alms:EmployeeStockPurchasePlan2024Member2024-06-300001847367alms:PerformanceOptionPlan2024Member2024-05-3100018473672023-12-310001847367us-gaap:FairValueInputsLevel1Memberus-gaap:FairValueMeasurementsRecurringMemberus-gaap:MoneyMarketFundsMember2025-09-300001847367us-gaap:FairValueMeasurementsRecurringMemberus-gaap:MoneyMarketFundsMember2025-09-300001847367us-gaap:FairValueInputsLevel1Memberus-gaap:FairValueMeasurementsRecurringMemberus-gaap:MoneyMarketFundsMember2024-12-310001847367us-gaap:FairValueMeasurementsRecurringMemberus-gaap:MoneyMarketFundsMember2024-12-3100018473672024-09-300001847367alms:AcelyrinIncMember2025-05-222025-09-300001847367alms:AcelyrinIncMemberus-gaap:GeneralAndAdministrativeExpenseMember2025-07-012025-09-300001847367alms:AcelyrinIncMember2025-07-012025-09-300001847367alms:AcelyrinIncMemberus-gaap:GeneralAndAdministrativeExpenseMember2025-01-012025-09-300001847367alms:AcelyrinIncMember2025-01-012025-09-300001847367alms:AcelyrinIncMemberus-gaap:AcquisitionRelatedCostsMember2024-07-012024-09-300001847367alms:AcelyrinIncMemberus-gaap:AcquisitionRelatedCostsMember2024-01-012024-09-300001847367srt:MaximumMemberalms:AcelyrinIncMemberalms:BusinessCombinationProFormaInformationNonrecurringAdjustmentStockBasedCompensationMember2024-07-012024-09-300001847367alms:AcelyrinIncMemberalms:BusinessCombinationProFormaInformationNonrecurringAdjustmentSeveranceCashObligationsMemberus-gaap:EmployeeSeveranceMember2024-07-012024-09-300001847367alms:AcelyrinIncMemberalms:BusinessCombinationProFormaInformationNonrecurringAdjustmentGainOnBargainPurchaseMember2024-07-012024-09-300001847367alms:AcelyrinIncMemberalms:BusinessCombinationProFormaInformationNonrecurringAdjustmentSeveranceCashObligationsMemberus-gaap:EmployeeSeveranceMember2024-01-012024-09-300001847367alms:AcelyrinIncMemberalms:BusinessCombinationProFormaInformationNonrecurringAdjustmentStockBasedCompensationMember2024-01-012024-09-300001847367alms:AcelyrinIncMemberalms:BusinessCombinationProFormaInformationNonrecurringAdjustmentGainOnBargainPurchaseMember2024-01-012024-09-300001847367us-gaap:USTreasurySecuritiesMember2025-09-300001847367us-gaap:CorporateDebtSecuritiesMember2025-09-300001847367us-gaap:CommercialPaperMember2025-09-300001847367alms:SupranationalDebtObligationsMember2025-09-300001847367alms:GovernmentDevelopmentBankObligationsMember2025-09-300001847367us-gaap:USTreasurySecuritiesMember2024-12-310001847367us-gaap:FairValueInputsLevel2Memberus-gaap:FairValueMeasurementsRecurringMember2025-09-300001847367us-gaap:FairValueInputsLevel1Memberus-gaap:FairValueMeasurementsRecurringMember2025-09-300001847367us-gaap:FairValueMeasurementsRecurringMember2025-09-300001847367us-gaap:FairValueInputsLevel2Memberus-gaap:FairValueMeasurementsRecurringMember2024-12-310001847367us-gaap:FairValueInputsLevel1Memberus-gaap:FairValueMeasurementsRecurringMember2024-12-310001847367us-gaap:FairValueMeasurementsRecurringMember2024-12-310001847367alms:FrontheraUsHoldingsIncAndFrontheraUsPharmaceuticalsLlcMemberalms:ClinicalMilestonesMember2021-03-310001847367alms:AcelyrinIncMember2023-07-310001847367alms:AcelyrinIncMember2023-01-310001847367us-gaap:RestrictedStockUnitsRSUMember2025-01-012025-09-300001847367us-gaap:EmployeeStockOptionMember2025-01-012025-09-300001847367us-gaap:EmployeeStockMember2025-01-012025-09-300001847367alms:UnvestedRestrictedCommonStockAndEarlyExercisedStockOptionsMember2025-01-012025-09-300001847367us-gaap:EmployeeStockOptionMember2024-01-012024-09-300001847367alms:UnvestedRestrictedCommonStockAndEarlyExercisedStockOptionsMember2024-01-012024-09-300001847367srt:MaximumMemberus-gaap:RestrictedStockMemberus-gaap:ShareBasedPaymentArrangementNonemployeeMember2025-07-012025-09-300001847367us-gaap:ShareBasedPaymentArrangementNonemployeeMember2025-07-012025-09-300001847367us-gaap:RestrictedStockUnitsRSUMember2025-07-012025-09-300001847367us-gaap:ResearchAndDevelopmentExpenseMember2025-07-012025-09-300001847367us-gaap:GeneralAndAdministrativeExpenseMember2025-07-012025-09-300001847367us-gaap:EmployeeStockOptionMember2025-07-012025-09-300001847367us-gaap:EmployeeStockMember2025-07-012025-09-300001847367srt:MaximumMemberus-gaap:RestrictedStockMemberus-gaap:ShareBasedPaymentArrangementNonemployeeMember2025-01-012025-09-300001847367us-gaap:ShareBasedPaymentArrangementNonemployeeMember2025-01-012025-09-300001847367us-gaap:RestrictedStockMember2025-01-012025-09-300001847367us-gaap:ResearchAndDevelopmentExpenseMember2025-01-012025-09-300001847367us-gaap:GeneralAndAdministrativeExpenseMember2025-01-012025-09-300001847367us-gaap:EmployeeStockOptionMember2025-01-012025-09-300001847367us-gaap:EmployeeStockMember2025-01-012025-09-300001847367srt:MaximumMemberus-gaap:RestrictedStockMemberus-gaap:ShareBasedPaymentArrangementNonemployeeMember2024-07-012024-09-300001847367us-gaap:ShareBasedPaymentArrangementNonemployeeMember2024-07-012024-09-300001847367us-gaap:RestrictedStockMember2024-07-012024-09-300001847367us-gaap:ResearchAndDevelopmentExpenseMember2024-07-012024-09-300001847367us-gaap:GeneralAndAdministrativeExpenseMember2024-07-012024-09-300001847367us-gaap:EmployeeStockOptionMember2024-07-012024-09-300001847367srt:MaximumMemberus-gaap:RestrictedStockMemberus-gaap:ShareBasedPaymentArrangementNonemployeeMember2024-01-012024-09-300001847367us-gaap:ShareBasedPaymentArrangementNonemployeeMember2024-01-012024-09-300001847367us-gaap:RestrictedStockMember2024-01-012024-09-300001847367us-gaap:ResearchAndDevelopmentExpenseMember2024-01-012024-09-300001847367us-gaap:GeneralAndAdministrativeExpenseMember2024-01-012024-09-300001847367us-gaap:EmployeeStockOptionMember2024-01-012024-09-300001847367us-gaap:IPOMember2024-07-012024-09-300001847367alms:ForesiteLabsMemberus-gaap:RelatedPartyMember2025-09-300001847367alms:ForesiteLabsMemberus-gaap:RelatedPartyMember2024-12-310001847367alms:KakenPharmaceuticalCo.LtdMembersrt:MaximumMemberalms:CollaborativeArrangementForProductEsk001Member2025-09-300001847367us-gaap:NonvotingCommonStockMember2025-11-060001847367alms:VotingCommonStockMember2025-11-060001847367alms:SeriesCRedeemableConvertiblePreferredStockMember2024-05-012024-05-310001847367alms:SeriesCRedeemableConvertiblePreferredStockMember2024-04-012024-06-300001847367alms:SeriesCRedeemableConvertiblePreferredStockMember2024-01-012024-03-310001847367us-gaap:AdditionalPaidInCapitalMember2025-07-012025-09-3000018473672025-07-012025-09-300001847367us-gaap:AdditionalPaidInCapitalMember2025-04-012025-06-3000018473672025-04-012025-06-300001847367us-gaap:AdditionalPaidInCapitalMember2025-01-012025-03-3100018473672025-01-012025-03-310001847367us-gaap:AdditionalPaidInCapitalMember2024-04-012024-06-3000018473672024-04-012024-06-300001847367us-gaap:AdditionalPaidInCapitalMember2024-01-012024-03-3100018473672024-01-012024-03-310001847367alms:EquityIncentivePlan2024Member2024-06-2700018473672024-03-292024-03-290001847367alms:EarlyExercisableEmployeeStockOptionsMember2025-09-300001847367alms:EarlyExercisableEmployeeStockOptionsMember2024-12-310001847367alms:PerformanceBasedRestrictedStockUnitsMemberalms:AcelyrinIncMember2025-05-210001847367alms:TwoThousandTwentyOneStockPlanMember2025-09-300001847367alms:PerformanceOptionPlan2024Member2025-01-012025-09-300001847367alms:StockOptionPlansExcludingPerformanceOptionPlan2024Member2025-01-012025-09-300001847367alms:MergerClosesBeforeMay152025Memberalms:PerformanceBasedRestrictedStockUnitsMemberalms:AcelyrinIncMember2025-05-210001847367alms:NonStatutoryOptionMemberalms:PerformanceOptionPlan2024Member2024-05-012024-05-310001847367us-gaap:RestrictedStockUnitsRSUMemberalms:AcelyrinIncMember2025-05-212025-05-210001847367alms:PerformanceBasedRestrictedStockUnitsMemberalms:AcelyrinIncMember2025-05-212025-05-210001847367us-gaap:RestrictedStockUnitsRSUMember2025-01-012025-09-300001847367us-gaap:RestrictedStockMemberus-gaap:ShareBasedPaymentArrangementNonemployeeMember2021-02-012021-02-280001847367srt:MinimumMemberalms:PerformanceOptionPlan2024Member2025-01-012025-09-300001847367srt:MaximumMemberalms:PerformanceOptionPlan2024Member2025-01-012025-09-300001847367alms:EmployeeStockPurchasePlan2024Member2024-06-012024-06-300001847367alms:AcelyrinIncMemberus-gaap:EmployeeSeveranceMember2025-05-212025-05-210001847367alms:AcelyrinIncMemberus-gaap:EmployeeSeveranceMember2025-05-210001847367us-gaap:CommonStockMember2025-04-012025-06-300001847367alms:ForesiteLabsMemberus-gaap:RelatedPartyMember2025-01-012025-09-300001847367alms:KakenPharmaceuticalCo.LtdMemberalms:CollaborativeArrangementForProductEsk001Member2025-03-012025-03-3100018473672023-01-012023-12-3100018473672022-01-012022-12-310001847367us-gaap:OtherNoncurrentAssetsMember2025-09-300001847367us-gaap:PrepaidExpensesAndOtherCurrentAssetsMember2025-09-300001847367us-gaap:PrivatePlacementMember2024-07-172024-07-170001847367alms:LegacyAlumisIncMember2025-01-310001847367alms:LegacyAcelyrinIncMember2025-01-310001847367alms:EquityIncentivePlan2024Member2024-06-272024-06-270001847367us-gaap:IPOMember2024-07-012024-07-0100018473672024-03-130001847367alms:SeriesCRedeemableConvertiblePreferredStockMember2024-03-012024-03-3100018473672024-03-012024-03-310001847367us-gaap:NonvotingCommonStockMember2024-07-012024-09-300001847367alms:VotingCommonStockMember2024-07-012024-09-300001847367srt:MaximumMembersrt:DirectorMemberus-gaap:ShareBasedPaymentArrangementNonemployeeMemberalms:EquityIncentivePlan2024Member2024-06-272024-06-270001847367srt:MaximumMembersrt:DirectorMemberus-gaap:ShareBasedPaymentArrangementNonemployeeMemberalms:EquityIncentivePlan2024Member2024-06-262024-06-2600018473672023-01-3100018473672022-08-310001847367alms:KakenPharmaceuticalCo.LtdMemberalms:GlobalDevelopmentCostReimbursementDermatologyFieldThroughEndOf2026Memberalms:CollaborativeArrangementForProductEsk001Member2025-03-310001847367alms:KakenPharmaceuticalCo.LtdMemberalms:GlobalDevelopmentCostReimbursementDermatologyFieldAfter2026Memberalms:CollaborativeArrangementForProductEsk001Member2025-03-310001847367alms:KakenPharmaceuticalCo.LtdMemberalms:CollaborativeArrangementForProductEsk001Member2025-03-3100018473672024-03-310001847367alms:AcelyrinIncMember2024-01-310001847367alms:SeriesCRedeemableConvertiblePreferredStockMember2024-05-310001847367us-gaap:CommonClassBMember2024-07-010001847367us-gaap:CommonClassAMember2024-07-010001847367us-gaap:CommonStockMember2024-07-012024-09-300001847367us-gaap:AdditionalPaidInCapitalMember2024-07-012024-09-3000018473672024-07-012024-09-300001847367alms:VotingCommonStockMember2025-09-300001847367alms:EquityIncentivePlan2024Member2025-01-012025-01-010001847367alms:EmployeeStockPurchasePlan2024Member2025-01-012025-01-010001847367alms:PierreFabreMemberalms:LicenseAndCommercializationAgreementMember2025-09-300001847367alms:PierreFabreMemberalms:LicenseAndCommercializationAgreementMember2021-03-252021-03-250001847367alms:PierreFabreMemberalms:LicenseAndCommercializationAgreementMember2021-03-250001847367alms:SingleReportableSegmentMember2025-07-012025-09-300001847367alms:SingleReportableSegmentMember2025-01-012025-09-300001847367alms:SingleReportableSegmentMember2024-07-012024-09-300001847367alms:SingleReportableSegmentMember2024-01-012024-09-300001847367alms:AcelyrinIncMember2025-05-210001847367alms:AcelyrinIncMemberus-gaap:InProcessResearchAndDevelopmentMember2025-05-210001847367alms:AcelyrinIncMember2025-05-212025-05-210001847367alms:FrontheraUsHoldingsIncAndFrontheraUsPharmaceuticalsLlcMemberalms:ClinicalMilestonesMember2024-08-012024-08-310001847367alms:FrontheraUsHoldingsIncAndFrontheraUsPharmaceuticalsLlcMemberalms:ClinicalMilestonesMember2022-01-012022-12-310001847367srt:MaximumMemberalms:FrontheraUsHoldingsIncAndFrontheraUsPharmaceuticalsLlcMemberalms:ApprovalMilestonesMember2021-03-012021-03-310001847367alms:FrontheraUsHoldingsIncAndFrontheraUsPharmaceuticalsLlcMemberalms:ClinicalMilestonesMember2021-03-012021-03-310001847367alms:FrontheraUsHoldingsIncAndFrontheraUsPharmaceuticalsLlcMember2025-09-300001847367alms:AcelyrinIncMember2023-07-012023-07-310001847367alms:AcelyrinIncMember2023-01-012023-01-3100018473672025-09-3000018473672024-12-3100018473672025-01-012025-09-3000018473672024-01-012024-09-30alms:Dutr:sqftalms:Yalms:segmentiso4217:USDxbrli:purealms:leasexbrli:sharesiso4217:JPYalms:instrumentalms:itemiso4217:USDxbrli:sharesalms:installment

UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

FORM 10-Q

(Mark One)

☒QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES
EXCHANGE ACT OF 1934

For the quarterly period ended September 30, 2025

☐TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES
EXCHANGE ACT OF 1934

For the transition period from to

Commission File Number: 001-42143

Alumis Inc.

(Exact name of registrant as specified in its charter)


Delaware	86-1771129
(State or other jurisdiction of incorporation or organization)	(I.R.S. Employer Identification Number)

280 East Grand Avenue

South San Francisco, CA 94080

(Address of Principal Executive Offices)

(650) 231-6625

(Registrant’s telephone number)

Indicate by check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days. Yes ☒ No ☐

Indicate by check mark whether the registrant has submitted electronically every Interactive Data File required to be submitted pursuant to Rule 405 of Regulation S-T (§232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to submit such files). Yes ☒ No ☐

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, a smaller reporting company, or an emerging growth company. See the definitions of “large accelerated filer,” “accelerated filer,” “smaller reporting company,” and “emerging growth company” in Rule 12b-2 of the Exchange Act.


Large accelerated filer	☐	Accelerated filer	☐

Non-accelerated filer	☒	Smaller reporting company	☒	Emerging growth company	☒

If an emerging growth company, indicate by check mark if the registrant has elected not to use the extended transition period for complying with any new or revised financial accounting standards provided pursuant to Section 13(a) of the Exchange Act. ☐

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act). Yes ☐ No ☒

Securities registered pursuant to Section 12(b) of the Act:


Title of Each Class	Trading symbol	Name of Exchange on which registered
Common Stock, par value $0.0001 per share	ALMS	The Nasdaq Global Select Market

As of November 6, 2025, the registrant had 97,208,495 shares of voting common stock, $0.0001 par value per share, and 7,184,908 shares of non-voting common stock, $0.0001 par value per share, outstanding.

Table of Contents

TABLE OF CONTENTS

		Page

Part I	Financial Information

Item 1.	Financial Statements (Unaudited)	5

	Condensed Consolidated Balance Sheets	5

	Condensed Consolidated Statements of Operations and Comprehensive Loss	6

	Condensed Consolidated Statements of Redeemable Convertible Preferred Stock and Stockholders’ Equity (Deficit)	7

	Condensed Consolidated Statements of Cash Flows	9

	Notes to Condensed Consolidated Financial Statements	10

Item 2.	Management’s Discussion and Analysis of Financial Condition and Results of Operations	41

Item 3.	Quantitative and Qualitative Disclosures about Market Risk	59

Item 4.	Controls and Procedures	60

Part II	Other Information

Item 1.	Legal Proceedings	61

Item 1A.	Risk Factors	61

Item 2.	Unregistered Sales of Equity Securities and Use of Proceeds	126

Item 3.	Defaults Upon Senior Securities	127

Item 4.	Mine Safety Disclosures	127

Item 5.	Other Information	127

Item 6.	Exhibits	127

Signatures		129

In this Quarterly Report on Form 10-Q, unless otherwise stated or as the context otherwise requires, references to “Alumis,” “the Company,” “we,” “us,” “our” and similar references refer to Alumis Inc.

This Quarterly Report on Form 10-Q also contains registered marks, trademarks and trade names of other companies. All other trademarks, registered marks and trade names appearing in this report are the property of their respective holders. We do not intend our use or display of other companies’ trade names, trademarks or service marks to imply a relationship with, or endorsement or sponsorship of us by, these other companies.

Table of Contents

SPECIAL NOTE REGARDING FORWARD-LOOKING STATEMENTS

This Quarterly Report on Form 10-Q contains forward-looking statements that are based on our management’s beliefs and assumptions and on information currently available to our management. All statements, other than statements of historical facts contained in this Quarterly Report on Form 10-Q, including statements regarding our future financial condition, business strategy and plans, and objectives of management for future operations, are forward-looking statements. In some cases, you can identify forward-looking statements by the following words: “anticipate,” “believe,” “continue,” “could,” “estimate,” “expect,” “intend,” “may,” “ongoing,” “plan,” “potential,” “predict,” “project,” “should,” “will,” “would” or the negative of these terms or other comparable terminology, although not all forward-looking statements contain these words.

These forward-looking statements involve risks, uncertainties and other factors that may cause our actual results, levels of activity, performance or achievements to be materially different from the information expressed or implied by these forward-looking statements. Although we believe that we have a reasonable basis for each forward-looking statement contained in this Quarterly Report on Form 10-Q, we caution you that these statements are based on a combination of facts and factors currently known by us and our projections of the future, about which we cannot be certain. Forward-looking statements in this Quarterly Report on Form 10-Q include, but are not limited to, statements about:

●	our expectations regarding the potential benefits of our strategy, including with respect to the integration of operations, technologies and personnel associated with the ACELYRIN Merger (as defined below);

●	our plans relating to the research and development of our product candidates;

●	developments related to our competitors and our industry, including the success of competing product candidates and therapies that are, or may become, available;

●	details regarding our strategic vision and planned product candidate pipeline;

●	our beliefs regarding the success, cost and timing of our product candidate development activities and current and future clinical trials and studies, including study design;

●	the timing or likelihood of regulatory filings or other actions and related regulatory authority responses;

●	the ability and willingness of various third parties to engage in research and development activities involving our product candidates, and our ability to leverage those activities;

●	our expectations regarding the potential benefits from any existing or future license or collaboration agreements, including the receipt of potential co-development, milestone and royalty payments

●	our expectations regarding the ease of administration associated with our product candidates;

●	our expectations regarding the patient compatibility associated with our product candidates;

●	our beliefs regarding the potential markets for our product candidates and our ability to serve those markets;

●	our beliefs regarding the potential of our product candidates to demonstrate differentiation from other approved therapies or therapies in development;

●	the ability to obtain and, if approved, maintain regulatory approval of any of our product candidates, and any related restrictions, limitations and/or warnings in the label of any approved product candidate;

●	our ability to commercialize any approved products;

Table of Contents

●	the rate and degree of market acceptance of any approved products;

●	our ability to attract and retain key personnel;

●	the accuracy of our estimates regarding our future revenue, as well as our future operating expenses, capital requirements and needs for additional financing;

●	our ability to obtain funding for our operations, including funding necessary to complete further development and any commercialization of our product candidates;

●	our ability to obtain, maintain, protect and enforce intellectual property protection for our product candidates and technology and not infringe, misappropriate or otherwise violate the intellectual property of others;

●	regulatory developments in the United States and foreign countries;

●

our expectations regarding the period during which we qualify as an “emerging growth company” under the Jumpstart Our Business Startups Act of 2012, as amended (the “JOBS Act”), and a “smaller reporting company,” as defined in Rule 12b-2 of the Securities Exchange Act of 1934, as amended (the “Exchange Act”); and

●	statements of belief and any statement of assumptions underlying any of the foregoing.

You should refer to the section titled “Risk Factors” in Part II, Item 1A. of this Quarterly Report on Form 10-Q for a discussion of other important factors that may cause our actual results to differ materially from those expressed or implied by our forward-looking statements. As a result of these factors, we cannot assure you that the forward-looking statements in this Quarterly Report on Form 10-Q will prove to be accurate.

In addition, statements that “we believe” and similar statements reflect our beliefs and opinions on the relevant subject. These statements are based upon information available to us as of the date of this Quarterly Report on Form 10-Q, and although we believe such information forms a reasonable basis for such statements, such information may be limited or incomplete, and our statements should not be read to indicate that we have conducted a thorough inquiry into, or review of, all potentially available relevant information. These statements are inherently uncertain, and investors are cautioned not to unduly rely upon these statements.

Furthermore, if our forward-looking statements prove to be inaccurate, the inaccuracy may be material. In light of the significant uncertainties in these forward-looking statements, you should not regard these statements as a representation or warranty by us or any other person that we will achieve our objectives and plans in any specified time frame, or at all. We undertake no obligation to publicly update any forward-looking statements, whether as a result of new information, future events or otherwise, except as required by law.

Table of Contents

PART I—FINANCIAL INFORMATION

Item 1. Financial Statements (Unaudited)

ALUMIS INC.

CONDENSED CONSOLIDATED BALANCE SHEETS

(Unaudited)


	September 30,		December 31,
(in thousands, except share and per share amounts)	2025		2024
Assets
Current assets:
Cash and cash equivalents	$	65,257	$	169,526
Marketable securities		312,467		118,737
Research and development prepaid expenses		4,955		13,424
Other prepaid expenses and current assets		10,611		4,501
Total current assets		393,290		306,188
Restricted cash, non-current		1,372		1,106
Property and equipment, net		19,058		20,968
Intangible assets		50,959		—
Operating lease right-of-use assets, net		17,511		12,723
Other assets, non-current		5,824		7
Total assets	$	488,014	$	340,992
Liabilities and Stockholders’ Equity
Current liabilities:
Accounts payable	$	4,554	$	9,624
Research and development accrued expenses		37,629		29,149
Other accrued expenses and current liabilities		18,821		10,580
Operating lease liabilities, current		4,412		1,557
Total current liabilities		65,416		50,910
Operating lease liabilities, non-current		33,385		29,165
Deferred revenue, non-current		1,944		—
Deferred income tax liability		2,140		—
Share repurchase liability		187		813
Other liabilities, non-current		169		—
Total liabilities		103,241		80,888
Commitments and contingencies (Note 9)
Stockholders’ equity:
Preferred stock, $0.0001 par value; 50,000,000 shares authorized, zero shares issued and outstanding as of September 30, 2025 and December 31, 2024		—		—
Common stock, voting, $0.0001 par value; 492,815,092 voting shares authorized as of September 30, 2025 and December 31, 2024; 97,174,231 and 47,222,419 voting shares issued and outstanding as of September 30, 2025 and December 31, 2024, respectively		9		4
Common stock, non-voting, $0.0001 par value; 7,184,908 non-voting shares authorized as of September 30, 2025 and December 31, 2024; 7,184,908 non-voting shares issued and outstanding as of September 30, 2025 and December 31, 2024		1		1
Additional paid-in capital		1,193,474		918,610
Accumulated other comprehensive income (loss)		234		40
Accumulated deficit		(808,945)		(658,551)
Total stockholders’ equity		384,773		260,104
Total liabilities and stockholders’ equity	$	488,014	$	340,992

The accompanying notes are an integral part of these unaudited condensed consolidated financial statements.

Table of Contents

ALUMIS INC.

CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS AND

COMPREHENSIVE LOSS

(Unaudited)


	Three Months Ended September 30,				Nine Months Ended September 30,
(in thousands, except share and per share amounts)	2025		2024		2025		2024
Revenue:
License revenue	$	—	$	—	$	17,389	$	—
Collaboration revenue		2,066		—		4,732		—
Total revenue		2,066		—		22,121		—
Operating expenses:
Research and development expenses, including related party expenses of $287, $160, $808 and $731 for the three and nine months ended September 30, 2025 and 2024, respectively		97,836		87,824		303,213		178,350
General and administrative expenses		19,522		10,575		76,267		23,782
Total operating expenses		117,358		98,399		379,480		202,132
Loss from operations		(115,292)		(98,399)		(357,359)		(202,132)
Other income (expense):
Gain on bargain purchase		—		—		187,907		—
Interest income		4,594		5,322		10,633		8,153
Change in fair value of derivative liability		—		—		—		(5,406)
Other income (expenses), net		(54)		(40)		(136)		(89)
Total other income (expense), net		4,540		5,282		198,404		2,658
Net loss before income taxes		(110,752)		(93,117)		(158,955)		(199,474)
Income tax benefit		—		—		8,561		—
Net loss	$	(110,752)	$	(93,117)	$	(150,394)	$	(199,474)
Other comprehensive income (loss):
Unrealized gain (loss) on marketable securities, net		212		140		194		137
Total comprehensive loss	$	(110,540)	$	(92,977)	$	(150,200)	$	(199,337)
Net loss per share attributable to common stockholders, basic and diluted	$	(1.06)	$	(1.73)	$	(1.92)	$	(10.15)
Weighted-average shares of common stock outstanding, basic and diluted		104,109,243		53,752,223		78,471,407		19,647,690

The accompanying notes are an integral part of these unaudited condensed consolidated financial statements.

Table of Contents

ALUMIS INC.

CONDENSED CONSOLIDATED STATEMENTS OF REDEEMABLE CONVERTIBLE PREFERRED STOCK AND STOCKHOLDERS’ EQUITY (DEFICIT)

(Unaudited)


	Redeemable								Accumulated
	Convertible						Additional		Other				Total
	Preferred Stock			Common Stock			Paid-In		Comprehensive		Accumulated		Stockholders’
(in thousands, except share amounts)	Shares	Amount		Shares	Amount		Capital		Income (Loss)		Deficit		Equity
Balance at December 31, 2024	—	$	—	54,407,327	$	5	$	918,610	$	40	$	(658,551)	$	260,104
Vesting of early exercised stock options	—		—	—		—		224		—		—		224
Vesting of restricted shares of common stock	—		—	—		—		2		—		—		2
Stock-based compensation expense	—		—	—		—		6,995		—		—		6,995
Other comprehensive income (loss), net	—		—	—		—		—		(48)		—		(48)
Net income (loss)	—		—	—		—		—		—		(98,963)		(98,963)
Balance at March 31, 2025	—	$	—	54,407,327	$	5	$	925,831	$	(8)	$	(757,514)	$	168,314

Issuance of common stock and equity awards in connection with the ACELYRIN Merger	—		—	48,653,549		5		238,072		—		—		238,077
Issuance of common stock upon vesting of RSUs	—		—	798,751		—		—		—		—		—
Issuance of common stock under the 2024 ESPP	—		—	184,633		—		766		—		—		766
Vesting of early exercised stock options	—		—	—		—		184		—		—		184
Repurchase of unvested early exercised stock options	—		—	(1,783)		—		—		—		—		—
Stock-based compensation expense	—		—	—		—		18,635		—		—		18,635
Other comprehensive income (loss), net	—		—	—		—		—		30		—		30
Net income (loss)	—		—	—		—		—		—		59,321		59,321
Balance at June 30, 2025	—	$	—	104,042,477	$	10	$	1,183,488	$	22	$	(698,193)	$	485,327

Issuance of common stock upon vesting of RSUs	—		—	316,662		—		—		—		—		—
Vesting of early exercised stock options	—		—	—		—		199		—		—		199
Stock-based compensation expense	—		—	—		—		9,787		—		—		9,787
Other comprehensive income (loss), net	—		—	—		—		—		212		—		212
Net income (loss)	—		—	—		—		—		—		(110,752)		(110,752)
Balance at September 30, 2025	—	$	—	104,359,139	$	10	$	1,193,474	$	234	$	(808,945)	$	384,773

The accompanying notes are an integral part of these unaudited condensed consolidated financial statements.

Table of Contents

ALUMIS INC.

CONDENSED CONSOLIDATED STATEMENTS OF REDEEMABLE CONVERTIBLE PREFERRED STOCK AND STOCKHOLDERS’ EQUITY (DEFICIT)

(Unaudited)


	Redeemable								Accumulated
	Convertible						Additional		Other				Total
	Preferred Stock			Common Stock			Paid-In		Comprehensive		Accumulated		Stockholders’
(in thousands, except share amounts)	Shares	Amount		Shares	Amount		Capital		Income (Loss)		Deficit		Equity (Deficit)
Balance at December 31, 2023	85,960,088	$	375,370	2,675,979	$	1	$	25,055	$	2	$	(364,318)	$	(339,260)
Issuance of Series C redeemable convertible preferred stock in March 2024 for cash, net of derivative liability of $8,913 and offering costs of $382	41,264,891		120,205	—		—		—		—		—		—
Issuance of common stock upon exercise of stock options and early exercised stock options	—		—	3,186		—		29		—		—		29
Vesting of early exercised stock options	—		—	—		—		494		—		—		494
Vesting of restricted shares of common stock	—		—	—		—		6		—		—		6
Stock-based compensation expense	—		—	—		—		2,657		—		—		2,657
Other comprehensive income (loss), net	—		—	—		—		—		(3)		—		(3)
Net loss	—		—	—		—		—		—		(49,849)		(49,849)
Balance at March 31, 2024	127,224,979	$	495,575	2,679,165	$	1	$	28,241	$	(1)	$	(414,167)	$	(385,926)

Issuance of Series C redeemable convertible preferred stock for cash and settlement of the derivative liability of $14,319, net of issuance costs of $157	41,264,892		143,662	—		—		—		—		—		—
Issuance of common stock upon exercise of stock options and early exercise of stock options	—		—	62,333		—		287		—		—		287
Vesting of early exercised stock options	—		—	—		—		253		—		—		253
Vesting of restricted shares of common stock	—		—	—		—		6		—		—		6
Stock-based compensation expense	—		—	—		—		3,133		—		—		3,133
Net loss	—		—	—		—		—		—		(56,508)		(56,508)
Balance at June 30, 2024	168,489,871	$	639,237	2,741,498	$	1	$	31,920	$	(1)	$	(470,675)	$	(438,755)

Issuance of voting common stock upon initial public offering, net of underwriting discounts and commissions and other offering costs of $16,684	—		—	13,125,000		1		193,315		—		—		193,316
Issuance of voting common stock in private placement transaction	—		—	2,500,000		—		40,000		—		—		40,000
Conversion and redesignation of redeemable convertible preferred stock into 28,855,656 shares of voting common stock and 7,184,908 shares of non-voting common stock in connection with initial public offering	(168,489,871)		(639,237)	36,040,564		3		639,234		—		—		639,237
Issuance of common stock upon exercise of stock options and early exercise of stock options	—		—	6,143		—		54		—		—		54
Vesting of early exercised stock options	—		—	—		—		201		—		—		201
Vesting of restricted shares of common stock	—		—	—		—		4		—		—		4
Repurchase of unvested shares of restricted common stock	—		—	(6,417)		—		—		—		—		—
Stock-based compensation expense	—		—	—		—		7,309		—		—		7,309
Other comprehensive income (loss), net	—		—	—		—		—		140		—		140
Net loss	—		—	—		—		—		—		(93,117)		(93,117)
Balance at September 30, 2024	—	$	—	54,406,788	$	5	$	912,037	$	139	$	(563,792)	$	348,389

The accompanying notes are an integral part of these unaudited condensed consolidated financial statements.

Table of Contents

ALUMIS INC.

CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS

(Unaudited)


	Nine Months Ended September 30,
(in thousands)	2025		2024
Cash flows from operating activities
Net loss	$	(150,394)	$	(199,474)
Adjustments to reconcile net loss to net cash used in operating activities:
Stock-based compensation		35,417		13,099
Net accretion of discounts on marketable securities		(3,876)		(1,987)
Depreciation and amortization		2,629		2,332
Non-cash lease expense		1,161		31
Loss on disposal of fixed assets		—		5
Change in fair value of derivative liability		—		5,406
Gain on bargain purchase in connection with the ACELYRIN Merger		(187,907)		—
Impairment of long-lived assets		529		—
Changes in operating assets and liabilities:
Research and development prepaid expenses		9,426		(9,581)
Other prepaid expenses and other assets		13,346		(1,605)
Other assets, non-current		(5,073)		—
Accounts payable		(11,586)		5,322
Deferred revenue		1,944		—
Research and development accrued expenses		4,935		7,193
Other accrued expenses and current liabilities		2,554		426
Operating lease liabilities		(2,328)		(1,481)
Other liabilities, non-current		168		—
Deferred income tax liability		(8,561)		—
Net cash used in operating activities		(297,616)		(180,314)
Cash flows from investing activities
Maturities of marketable securities		305,423		42,000
Purchases of marketable securities		(161,648)		(185,374)
Purchases of property and equipment		(653)		(1,366)
Cash, cash equivalents and restricted cash acquired in connection with the ACELYRIN Merger		49,742		—
Net cash provided by (used in) investing activities		192,864		(144,740)
Cash flows from financing activities
Proceeds from issuance of redeemable convertible preferred stock and derivative liability, net of issuance costs		—		258,461
Proceeds from initial public offering, net of underwriter discounts and commissions and other offering costs		—		193,316
Proceeds from a private placement transaction		—		40,000
Proceeds from issuance of common stock upon exercise of stock options		—		591
Repurchase of common stock shares issued upon early exercised restricted common stock		(17)		(6)
Proceeds from issuance of common stock under the 2024 ESPP		766		—
Net cash provided by financing activities		749		492,362
Net (decrease) increase in cash, cash equivalents and restricted cash		(104,003)		167,308
Cash, cash equivalents and restricted cash at beginning of period		170,632		47,133
Cash, cash equivalents and restricted cash at end of period	$	66,629	$	214,441
Supplemental disclosures:
Conversion of 168,489,871 shares of redeemable convertible preferred stock upon the closing of initial public offering	$	—	$	639,237
Equity consideration transferred in connection with the ACELYRIN Merger	$	238,077	$	—
Vesting of early exercised stock options and unvested restricted shares of common stock	$	609	$	964
Purchases of property and equipment in other accrued expenses and current liabilities	$	—	$	6
Right-of-use assets obtained in exchange for operating lease liabilities	$	1,776	$	—
Recognition of derivative liability upon issuance of redeemable convertible preferred stock	$	—	$	8,913
Settlement of derivative liability upon issuance of redeemable convertible preferred stock	$	—	$	(14,319)

Reconciliation of cash, cash equivalents and restricted cash:
Cash and cash equivalents	$	65,257	$	213,417
Restricted cash, non-current		1,372		1,024
Total cash, cash equivalents and restricted cash	$	66,629	$	214,441

The accompanying notes are an integral part of these unaudited condensed consolidated financial statements.

Table of Contents

ALUMIS INC.

NOTES TO THE CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

(Unaudited)

1.	Organization and Nature of the Business

Organization and Business

Alumis Inc. (the “Company”) is a clinical stage biopharmaceutical company focused on identifying, acquiring, and accelerating the development and commercialization of transformative medicines for autoimmune disorders. The Company leverages its proprietary precision data analytics platform, biological insights, and a team of experts with deep experience in precision medicine drug discovery, development, and immunology, in its mission to create medicines that significantly improve the lives of patients by replacing broad immunosuppression with targeted therapies.

The Company was founded on January 29, 2021, as a Delaware corporation under the name FL2021-001, Inc. FL2021-001, Inc.’s name was changed to Esker Therapeutics, Inc. on March 8, 2021, and to Alumis Inc. on January 6, 2022. The Company is headquartered in South San Francisco, California. As of September 30, 2025, the Company had one wholly owned subsidiary, ACELYRIN, Inc. (“ACELYRIN”), a Delaware corporation incorporated on July 27, 2020 and its wholly owned subsidiary, WH2, LLC. Arrow Merger Sub, Inc. (“Merger Sub”), the Company’s wholly owned subsidiary incorporated in January 2025, was merged with and into ACELYRIN in May 2025.

Initial Public Offering and Concurrent Private Placement

On July 1, 2024, the Company completed its initial public offering (“IPO”), pursuant to which it issued and sold 13,125,000 shares of its common stock at $16.00 price per share to the public. Net proceeds from the IPO were $193.3 million, after deducting underwriting discounts and commissions and other offering costs totaling $16.7 million. On July 17, 2024, an existing investor and a holder of more than 5% of the Company’s capital stock, purchased an additional 2,500,000 shares of the Company’s common stock at the IPO price per share for total gross and net proceeds of $40.0 million in a private placement transaction (the “Concurrent Private Placement”).

Immediately prior to the closing of the IPO on July 1, 2024, all of the shares of the Company’s redeemable convertible preferred stock then outstanding converted into 28,855,656 shares of Class A common stock and 7,184,908 shares of Class B common stock at a 1-for-4.675 conversion ratio (the “Preferred Stock Conversion”). All outstanding Class A common stock shares and all outstanding Class B common stock shares were redesignated immediately thereafter into the same number of shares of voting common stock and non-voting common stock, respectively. Unless the context otherwise requires a different meaning, all references to “common stock” in these notes refers to the Company’s voting common stock and non-voting common stock combined.

ACELYRIN Merger

On February 6, 2025, the Company entered into an Agreement and Plan of Merger, and, on April 20, 2025, the Company entered into an Amendment to Agreement and Plan of Merger (collectively the “Merger Agreement”) with ACELYRIN and Merger Sub, a Delaware corporation and a direct wholly owned subsidiary of the Company. Under the terms of the Merger Agreement, Merger Sub merged with and into ACELYRIN, with ACELYRIN continuing as a direct wholly owned subsidiary of the Company (the “ACELYRIN Merger”). The Merger Agreement was approved by the disinterested directors on the Company’s board of directors and the board of directors of ACELYRIN and was approved by the stockholders of each company on May 13, 2025. On May 21, 2025, the Company completed the ACELYRIN Merger with ACELYRIN in a common stock transaction valued at approximately $238.1 million settled through the issuance of

ALUMIS INC.

NOTES TO THE CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

(Unaudited)

48,653,549 shares of the Company’s common stock to acquire net assets with a fair value of $426.0 million. See Note 3 for additional information.

Liquidity

The Company has incurred negative operating cash flows and significant losses from operations since its inception. For the three and nine months ended September 30, 2025 and 2024, the Company incurred net loss of $110.8 million, $93.1 million, $150.4 million and $199.5 million, respectively. Cash used in operating activities was $297.6 million and $180.3 million for the nine months ended September 30, 2025 and 2024, respectively. As of September 30, 2025, the Company had an accumulated deficit of $808.9 million.

The Company has historically funded its operations primarily through issuance of common stock, including in its IPO and Concurrent Private Placement, the issuance of redeemable convertible preferred stock and convertible promissory notes in private placements and, most recently, the acquisition of cash, cash equivalents and marketable securities in connection with the ACELYRIN Merger and payments received under its collaboration and license agreement with Kaken Pharmaceutical Co., Ltd. The Company expects to continue to incur substantial losses for the foreseeable future, and its ability to achieve and sustain profitability will depend on the successful development, approval, and commercialization of any product candidates it may develop, and on the achievement of sufficient revenue to support its cost structure. The Company may never achieve profitability and, unless and until it does, it will need to continue to raise additional capital. The Company believes that, based on its current operating plan, its existing cash, cash equivalents and marketable securities of $377.7 million as of September 30, 2025, will be sufficient to meet its operating and capital requirements for at least 12 months from the date of issuance of these unaudited condensed consolidated financial statements.

The Company will need to raise significant additional capital to fund ongoing research and development activities and maintain future operations. The Company’s management continuously monitors and, where necessary, may reduce its operating expenses in response to its clinical development progress and its ability and need to raise additional capital through a combination of public and private equity, debt financings, strategic alliances and licensing arrangements. For example, should any of the Company’s ongoing trials not meet its clinical development objectives, the Company may scale back or discontinue related activities and reallocate its working capital to extend its ability to meet its operating and capital requirements. The Company’s ability to access capital when needed is not assured and, if capital is not available to the Company when, and in the amounts, needed, on the terms which are favorable, the Company could be required to delay, scale back, or abandon some or all of its planned development programs and other operations, which could materially harm the Company’s business, financial condition and results of operations.

2.	Summary of Significant Accounting Policies and Basis of Presentation

The significant accounting policies and estimates used in the preparation of the accompanying unaudited condensed consolidated financial statements are described in the Company’s audited consolidated financial statements for the year ended December 31, 2024 included in the Company’s Annual Report on Form 10-K filed with the SEC on March 19, 2025. There have been no material changes in the Company’s significant accounting policies during the nine months ended September 30, 2025, except business combinations, acquired in-process research and development (“IPR&D”) intangible assets, collaboration arrangements, revenue recognition, stock-based compensation expense, and provision for income tax expense as discussed below.

Basis of Presentation

The condensed consolidated financial statements and accompanying notes are unaudited and have been prepared in accordance with accounting principles generally accepted in the United States of America (“U.S. GAAP”) and applicable rules and regulations of the SEC regarding interim financial reporting and do not contain all information that is included in the annual financial statements and notes thereto of the Company.

ALUMIS INC.

NOTES TO THE CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

(Unaudited)

The Company’s unaudited condensed consolidated financial statements include the accounts of its subsidiaries, and all intercompany transactions were eliminated. The Company’s unaudited condensed consolidated financial statements include the accounts of its subsidiaries ACELYRIN and WH2, LLC after the closing of the ACELYRIN Merger, and the accounts of Merger Sub from its incorporation in January 2025 until the ACELYRIN Merger. WH2, LLC has not had any operations or any balances from its inception. FronThera U.S. Holdings, Inc. and FronThera U.S. Pharmaceuticals LLC, two wholly owned subsidiaries, were dissolved on April 8, 2024 and March 14, 2024, respectively.

The unaudited condensed consolidated interim financial statements have been prepared on the same basis as the audited annual financial statements and, in the opinion of management, reflect all adjustments, which include only normal recurring adjustments necessary for the fair statement of the Company’s financial position as of September 30, 2025, its results of operations for the three and nine months ended September 30, 2025 and 2024 and its cash flows for the nine months ended September 30, 2025 and 2024. The condensed balance sheet as of December 31, 2024, included in this filing, was derived from audited annual consolidated financial statements but does not include all disclosures required by U.S. GAAP. The results of operations for the three and nine months ended September 30, 2025 and 2024 are not necessarily indicative of the results of operations to be expected for the full year or for any other subsequent interim period.

Any reference in these notes to applicable guidance is meant to refer to the authoritative U.S. GAAP as found in the Accounting Standards Codification (“ASC”) and Accounting Standards Updates (“ASU”) of the Financial Accounting Standards Board (“FASB”).

Use of Estimates

The preparation of financial statements in conformity with U.S. GAAP requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities, the disclosure of contingent assets and liabilities at the date of the financial statements and the reported amounts of expenses during the reporting period.

On an ongoing basis, the Company evaluates estimates and assumptions, including but not limited to those related to revenue recognition, accruals for research and development expenses, stock-based compensation expense, impairment of the IPR&D intangible assets, and the provision for income tax expense. Management bases its estimates on historical experience and on various other assumptions that are believed to be reasonable under the circumstances, the results of which form the basis for making judgments about the carrying values of assets and liabilities that are not readily apparent from other sources. Actual results may differ materially from those estimates.

Segment and Geographical Information

The Company operates and manages its business as one reportable and operating segment, which is the business of researching and developing medicines for autoimmune disorders. The chief executive officer, who is the chief operating decision maker (“CODM”), reviews financial information on an aggregate basis for purposes of allocating resources and evaluating financial performance. See Note 15 for additional information. All of the Company’s long-lived assets are located in the United States.

Concentration of Credit Risk

Financial instruments which potentially subject the Company to concentration of credit risk consist primarily of cash and cash equivalents, investments in marketable securities, accounts receivable and restricted cash. The Company maintains bank deposits in federally insured financial institutions and certain of these deposits exceed federally insured limits. To date, the Company has not experienced any losses on its deposits of cash and periodically evaluates the creditworthiness of the financial institutions at which its bank deposits are maintained.

The Company also invests in money market funds, U.S. Treasury obligations, commercial paper, corporate debt obligations, supranational debt obligations, government development bank obligations and Federal agency obligations,

ALUMIS INC.

NOTES TO THE CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

(Unaudited)

which can be subject to certain credit risks. The Company mitigates the risks by investing in high-grade instruments, limiting its exposure to any one issuer and monitoring the ongoing creditworthiness of the financial institutions and issuers. The Company has not experienced any loss of principal on its financial instruments.

Risks and Uncertainties

The Company is subject to certain risks and uncertainties, including, but not limited to, changes in any of the following areas that the Company believes could have a material adverse effect on the future financial position or results of operations: the Company’s ability to advance the development of its proprietary precision data analytics platform, timing and ability to advance its product candidates through preclinical and clinical development; costs and timelines associated with the manufacturing of clinical supplies; regulatory approval, market acceptance of, and reimbursement for, any product candidates the Company may develop; performance of third-party vendors; competition from pharmaceutical or other biotechnology companies with greater financial resources or expertise; protection of intellectual property; litigation or claims against the Company based on intellectual property or other factors; and its ability to attract and retain employees necessary to support its growth.

The Company’s business and results of operations may be affected by worldwide economic conditions, which may continue to be impacted by global macroeconomic challenges and uncertainty in the markets, including international trade policies and tariffs, severely diminished liquidity and credit availability, rising inflation and monetary supply shifts, rising interest rates, labor shortages, declines in consumer confidence, declines in economic growth, increases in unemployment rates, recession risks and uncertainty about economic and geopolitical stability (for example, related to the ongoing conflicts in Ukraine and the evolving U.S and ex-U.S. tariff landscape). These worldwide economic conditions have continued throughout 2025 and may negatively impact the Company’s business, financial position and results of operations.

Business Acquisitions, Including Intangible Assets, Goodwill and Contingent Consideration

The Company accounts for business combinations, as defined in ASC Topic 805, Business Combinations, using the acquisition method of accounting, which generally requires that assets acquired, including IPR&D intangible assets, and liabilities assumed, be recorded at fair value on the consolidated balance sheets as of the acquisition date. The excess of the fair value of the purchase consideration over the fair value of net assets acquired, if any, is recorded as goodwill on the consolidated balance sheet. The excess of the fair value of net assets acquired over the fair value of the purchase consideration, if any, represents negative goodwill, or a gain on bargain purchase, which is recognized in the consolidated statement of operations as of the date of the acquisition.

Calculating the fair value of assets acquired and liabilities assumed requires the Company to make significant estimates and assumptions. As a result, the Company may record adjustments to the fair values within the measurement period, which may be up to one year from the acquisition date, with the corresponding offset to goodwill or a gain on bargain purchase.

Transaction costs associated with business combinations are expensed as they are incurred.

Intangible assets related to IPR&D projects acquired are considered to be indefinite-lived until abandonment or completion of the associated R&D efforts, which generally occurs when regulatory approval is obtained. Goodwill and indefinite-lived intangible assets are not amortized and, instead, are tested for impairment annually, in the fourth quarter, or more frequently if events or changes in circumstances indicate that it is more likely than not that the assets are impaired. Development costs incurred after an acquisition are expensed as incurred.

Intangible assets with finite useful lives, which include completed IPR&D projects, are amortized over their estimated useful lives, primarily on a straight-line basis, and are also periodically reviewed for changes in facts or circumstances that may result in an impairment or in a reduction to the estimated useful life of the asset.

ALUMIS INC.

NOTES TO THE CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

(Unaudited)

In determining the initial fair value of an intangible asset, or when quantitative analysis is required to determine any impairment, the Company usually uses an income approach that discounts expected future cash flows to present value using a discount rate that is based on the estimated weighted-average cost of capital for comparable companies and represents the rate that market participants would use to value the intangible asset. These cash flow models require the use of Level 3 fair value measurements and inputs, including estimated revenues, costs and probabilities of technical and regulatory milestones, among other factors.

If the Company is required to pay future consideration that is contingent upon the achievement of specified development, regulatory approval or sales-based milestone events, then the estimated fair value of contingent consideration liabilities is recognized in the consolidated balance sheet as of the date of the acquisition. Each reporting period thereafter, the Company revalues these obligations and records increases or decreases in their fair value on the consolidated statements of operations until such time that the payment is made or obligations expire.

Collaboration Arrangements and Revenue Recognition

The Company earns revenue from collaboration agreements that allow collaborators to develop, manufacture and commercialize product candidates. Arrangements with collaborators may include intellectual property licenses, research and development services, manufacturing services for clinical and commercial supply and participation in joint steering committees. At the inception of an agreement, the Company evaluates if an agreement is a collaborative arrangement within the scope of ASC 808, Collaborative Arrangements (“ASC 808”). For collaborative arrangements that fall within the scope of ASC 808, the Company first determines which elements of the collaboration are deemed to be a performance obligation with a customer within the scope of ASC Topic 606, Revenue from Contracts with Customers (“ASC 606”). For elements of collaboration arrangements that are accounted for pursuant to ASC 808 and are not subject to the guidance in ASC 606, the Company applies the revenue recognition model under ASC 606 or other guidance, as deemed appropriate.

Under ASC 606, the Company recognizes revenue in an amount that reflects the consideration that the Company expects to receive in exchange for those goods or services when its collaborator, or customer, obtains control of promised goods or services. The Company follows a five-step approach: (i) identify the contract with a customer, (ii) identify the performance obligations in the contract, (iii) determine the transaction price, (iv) allocate the transaction price to the performance obligations and (v) recognize revenue when (or as) the customer obtains control of the product or service.

The Company assesses the goods or services promised within the contract to determine whether each promised good or service is a performance obligation. Performance obligations are promises in a contract to transfer a distinct good or service to the customer that (i) the customer can benefit from on its own or together with other readily available resources and (ii) are separately identifiable from other promises in the contract. Goods or services that are not individually distinct performance obligations are combined with other promised goods or services until such combined group of promises meet the requirements of a performance obligation.

The Company determines the transaction price based on the amount of consideration the Company is entitled to receive in exchange for the transfer of control of a product or a service to the customer. Consideration may be fixed, variable, or a combination of both. Payments to the Company under these arrangements typically include one or more of the following: non-refundable upfront payments, reimbursement for research services, payments for clinical supplies, research, development or regulatory milestone payments, profit-sharing arrangements, and royalty and commercial sales milestone payments. Variable consideration, such as performance-based milestones, are included in the total consideration if the Company expects to receive such consideration and if it is probable that the inclusion of the variable consideration will not result in a significant reversal in the cumulative amount of revenue recognized under the arrangement. The Company accounts for cost reimbursements included in the transaction price using the expected value method. The Company excludes sales-based royalty and milestone payments from the total consideration it expects to receive until the underlying sales occur because the license to its intellectual property is deemed to be the predominant item to which the royalties or milestones relate as it is the primary driver of value in the collaboration arrangements.

ALUMIS INC.

NOTES TO THE CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

(Unaudited)

The Company then allocates the transaction price to each distinct performance obligation based on the relative standalone selling price. Key assumptions to determine the standalone selling price may include forecasted revenues, development timelines, probabilities of technical and regulatory success, and the expected level of effort for research and development services. The Company recognizes revenue associated with each performance obligation as the control over the promised goods or services transfer to its collaborators which occurs either at a point in time or over time. If control transfers over time, revenue is recognized by using a method of measuring progress that best depicts the transfer of goods or services. The Company evaluates the measure of progress and related inputs each reporting period and any resulting adjustments to revenue are recorded on a cumulative catch-up basis. Consideration allocated to options that include material rights is deferred until the options are exercised or expire.

The Company records amounts as accounts receivable when the right to consideration is deemed unconditional. Consideration received that does not meet the requirements to satisfy ASC 606 revenue recognition criteria is recorded as deferred revenue in the consolidated balance sheets, classified as either current (less than 12 months) or non-current (more than 12 months) deferred revenue based on the Company’s best estimate of when such revenue will be recognized. See Note 7 for additional information.

Stock-Based Compensation Expense

The Company grants stock-based awards to employees, directors and non-employee consultants in the form of stock options and restricted stock units (“RSUs”) to purchase shares of its common stock. The Company measures stock options granted with service-based vesting based on the fair value of the award on the grant date using the Black-Scholes option-pricing model. The model requires management to make a number of assumptions, including common stock fair value, expected volatility, expected term, risk-free interest rate and expected dividend yield. The Company expenses the fair value of its stock-based compensation awards on a straight-line basis over the requisite service period, which is the period in which the related services are received.

The Company has also granted stock options with graded vesting based on market, service and performance conditions. At the grant date, the fair value of these stock options was estimated using a Monte Carlo simulation model, which uses a distribution of potential outcomes over the vesting period. The assumptions utilized in the calculation included the Company’s expected common stock price, expected volatility, risk-free rate and expected term. Stock-based compensation expense for these awards is recognized on a straight-line basis over the requisite service period, which is the longer of the explicit service period of the service condition and the derived service period of the market condition, as determined for each separately vesting portion of the awards as if each award was, in substance, multiple awards.

Stock-based compensation expense related to stock purchase rights under the Company’s 2024 Employee Stock Purchase Plan (the “2024 ESPP”) is measured based on grant date at fair value using the Black-Scholes option-pricing model. The model requires management to make a number of assumptions, including common stock fair value, expected volatility, expected term, risk-free interest rate and expected dividend yield. Stock-based compensation expense is recognized on a straight-line basis over the offering period.

The Company accounts for award forfeitures as they occur and classifies stock-based compensation expense in its consolidated statements of operations and comprehensive loss in the same manner in which the award recipient’s salary or services costs are classified.

Provision for Income Tax Expense

Income taxes are accounted for using the asset and liability method. Deferred tax assets and liabilities are recognized for the future tax consequences attributable to differences between the financial statements carrying amounts of existing assets and their respective tax bases. Deferred taxes and liabilities are measured using the enacted tax rates expected to apply to taxable income in the years in which those temporary differences are expected to be recovered or settled. The effect on deferred tax assets and liabilities of a change in tax rates is recognized in income in the period of enactment. The Company

ALUMIS INC.

NOTES TO THE CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

(Unaudited)

records a valuation allowance to reduce deferred tax assets to an amount for which realization is more likely than not. Due to the Company’s historical operating performance and the recorded cumulative net losses in prior fiscal periods, the net deferred tax assets have been fully offset by a valuation allowance.

The Company recognizes the tax benefit from an uncertain tax position if it is more likely than not that the tax position will be sustained upon examination by the tax authorities, based on the merits of the position. The Company’s policy is to recognize interest and penalties related to the underpayment of income taxes as a component of income tax expense or benefit. To date, there have been no interest or penalties incurred in relation to unrecognized tax benefits.

The Company recognized a benefit from income taxes of zero and $8.6 million for the three and nine months ended September 30, 2025, respectively, and zero for the three and nine months ended September 30, 2024. The income tax benefit is primarily related to the realization of deferred tax assets and valuation allowance release as a result of the ACELYRIN Merger.

On July 4, 2025, the One Big Beautiful Bill Act (the “OBBBA”) was enacted in the United States. The OBBBA includes significant provisions, including, but not limited to, modifications of capitalization of research and development expenses and accelerated fixed asset depreciation. The Company does not expect that the OBBBA will have a material impact on its consolidated financial statements for the fiscal year ending December 31, 2025.

Recoverable Value-Added Tax

The Company conducts clinical trials in several European and Asian countries which can result in VAT assessments based on the transfer of products across borders including production, packaging and distribution of clinical materials. VAT is a national tax that is levied at each stage of production and can vary by jurisdiction. When a company is not VAT-registered in a country, VAT is due when goods enter a country and is not considered reclaimable. When the Company becomes VAT-registered and establishes a pattern of VAT recoverability from taxing authorities in a certain country, the Company will record aggregate balances recoverable in other prepaid expenses and current assets in the consolidated balance sheets. The Company reviews these balances on a regular basis and records valuation allowances on the amounts that are not expected to be recovered.

Recent Accounting Pronouncements

From time to time, new accounting pronouncements are issued by the FASB or other standard setting bodies and adopted by the Company as of the specified effective date. The Company qualifies as an “emerging growth company” as defined in the JOBS Act, and has elected not to “opt out” of the extended transition related to complying with new or revised accounting standards, which means that when a standard is issued or revised and it has different application dates for public and private companies, the Company will adopt the new or revised standard at the time private companies adopt the new or revised standard and will do so until such time that the Company either (i) irrevocably elects to “opt out” of such extended transition period or (ii) no longer qualifies as an emerging growth company. The Company may choose to early adopt any new or revised accounting standards whenever such early adoption is permitted for private companies.

Recently Issued and Not Yet Adopted Accounting Pronouncements

In December 2023, the FASB issued ASU No. 2023-09, Income Taxes (Topic 740): Improvements to Income Tax Disclosures (“ASU 2023-09”), which requires the disclosure of specific categories in the rate reconciliation and greater disaggregation for income taxes paid. ASU 2023-09 is effective for annual periods beginning after December 15, 2024 for public entities and for fiscal years beginning after December 15, 2025 for all other entities, with early application permitted. ASU 2023-09 should be adopted prospectively with the option to be adopted retrospectively. The Company is currently evaluating the impact of this standard on its disclosure in its consolidated financial statements for the year ending December 31, 2025.

ALUMIS INC.

NOTES TO THE CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

(Unaudited)

In November 2024, the FASB issued ASU No. 2024-03, Disaggregation of Income Statement Expenses (Topic 220) (“ASU 2024-03”), requiring that public business entities disclose additional information about specific expense categories in the notes to financial statements at interim and annual reporting periods. The amendments of ASU 2024-03 are effective for annual reporting periods beginning after December 15, 2026, and interim reporting periods within annual periods beginning after December 15, 2027. The requirements of ASU 2024-03 may be applied either prospectively to financial statements issued for reporting periods after the effective date or retrospectively to any or all prior periods presented in the financial statements. The Company is currently evaluating the impact of adopting ASU 2024-03 on its consolidated financial statements and disclosures.

3.	Acquisitions

ACELYRIN Merger

The Company completed the ACELYRIN Merger on May 21, 2025 (the “Closing Date”). ACELYRIN was a late-stage biopharma company focused on identifying, acquiring, and accelerating the development and commercialization of transformative medicines. ACELYRIN’s portfolio consisted of lonigutamab, a subcutaneously delivered, monoclonal antibody targeting IGF-1R for the potential treatment of Thyroid Eye Disease (“TED”). The ACELYRIN Merger strengthened the Company’s balance sheet and its cash position and added the lonigutamab product candidate to the Company’s development portfolio as of the Closing Date. Immediately following the ACELYRIN Merger, the Company’s pre-merger stockholders collectively owned approximately 52% of the combined company’s common stock and the pre-merger stockholders of ACELYRIN owned approximately 48% of the combined company’s common stock, in each case, calculated on a fully diluted basis as of January 31, 2025.

As of the Closing Date, the Company (i) issued 48,653,549 shares of its common stock in exchange for ACELYRIN issued and outstanding common stock shares and paid cash for fractional shares, (ii) assumed ACELYRIN’s stock options with an exercise price of $18.00 or less outstanding and unexercised immediately prior to the Closing Date, which are exercisable into 4,712,186 shares of the Company’s common stock, (iii) assumed ACELYRIN’s RSUs outstanding and unvested immediately prior to the Closing Date, which were converted into 1,323,905 of the Company’s RSUs, and (iv) assumed ACELYRIN’s performance RSUs outstanding and unvested immediately prior to the Closing Date, which were converted into 146,963 of the Company’s RSUs subject only to a service vesting condition.

Outstanding shares, stock options, RSUs and performance RSUs were exchanged at the exchange ratio of 0.4814 shares of the Company’s common stock for each share of ACELYRIN common stock (the “Exchange Ratio”). ACELYRIN’s outstanding and unexercised options with exercise prices more than $18.00 were cancelled. Exercise prices for the assumed options were determined as the product of the original exercise prices multiplied by the reciprocal of the Exchange Ratio. Converted ACELYRIN stock options and RSUs continue to vest in accordance with their original terms. Performance RSUs were deemed to have 100% satisfied their performance conditions and will vest in two equal installments on May 15 of calendar years 2026 and 2027, subject to the holder of the converted performance RSUs remaining in service with the Company or any of its subsidiaries on such date.

ALUMIS INC.

NOTES TO THE CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

(Unaudited)

The preliminary purchase price consideration consists of the Company’s shares of common stock issued as of the Closing Date and the additional stock-based compensation related to the fair value of replacement awards attributable to pre-combination services, and is calculated as follows (in thousands, except share and per share data):


Implied shares of common stock issued to holders of ACELYRIN common stock		48,653,549
Closing price per share of common stock as of Closing Date	$	4.78
Consideration transferred for share exchange	$	232,564
Fair value of replacement awards attributable to pre-combination services	$	5,513
Total preliminary purchase price consideration	$	238,077

The ACELYRIN Merger was accounted for as a business combination with the Company being treated as the accounting acquirer. Net assets acquired were recognized at their fair value as of the Closing Date of the ACELYRIN Merger. The Company recognized ACELYRIN Merger transaction costs of $(0.1) and $14.7 million in general and administrative expenses in the unaudited condensed consolidated statements of operations and comprehensive loss for the three and nine months ended September 30, 2025, respectively.

The following table presents the preliminary purchase price allocation of the fair value of the net assets acquired and liabilities assumed as of the Closing Date (in thousands):


Assets Acquired
Cash and cash equivalents	$	49,155
Restricted cash		367
Marketable securities		333,436
Research and development prepaid expenses		958
Prepaid credit voucher for clinical manufacturing		11,376
Other prepaid expenses and current assets		8,081
Restricted cash, non-current		220
Property and equipment, net		420
Intangible assets		50,959
Operating lease right-of-use assets, net		4,349
Other assets, non-current		744
Total assets	$	460,065
Liabilities Assumed
Accounts payable	$	(6,518)
Research and development accrued expenses		(3,546)
Other accrued expenses and current liabilities		(5,688)
Operating lease liabilities, current		(1,390)
Operating lease liabilities, non-current		(6,238)
Deferred income tax liability		(10,701)
Total liabilities		(34,081)
Fair value of net assets	$	425,984
Purchase consideration		238,077
Gain on bargain purchase	$	187,907

Valuing certain components of the ACELYRIN Merger, primarily the acquired IPR&D intangible asset and a deferred income tax liability required the Company to make significant estimates that may be adjusted in the future; consequently, the purchase price allocation is considered preliminary. The preliminary fair value estimates of the net assets acquired are based upon preliminary calculations and valuations and are subject to change as the Company obtains additional information during the measurement period (up to one year from the Closing Date).

ALUMIS INC.

NOTES TO THE CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

(Unaudited)

Intangible assets represent the IPR&D intangible asset related to the acquired lonigutamab product candidate in development as of the Closing Date. The preliminary fair value of the acquired IPR&D intangible asset was estimated at $51.0 million using the multi-period excess earnings method which is equal to the present value of the incremental after-tax cash flows attributable to that intangible asset, using a discount rate of 23.0% based on the best estimate of a market participant's after-tax weighted average cost of capital. Projected future cash flows were based on significant estimates, including estimated revenues, costs and probabilities of technical and regulatory milestones, among other factors. The acquired IPR&D intangible asset is an indefinite-life asset and will be tested for impairment at least annually or whenever events or changes in circumstances indicate that the carrying value may not be recoverable as ASC 350 Intangibles - Goodwill and Other also requires testing more frequently if events or changes in circumstances indicate that it is more likely than not that the asset is impaired.

The Company acquired a prepaid credit voucher for clinical manufacturing issued by one of ACELYRIN’s contract manufacturers that will be applied towards payments of clinical product manufacturing invoices issued by the vendor. The remaining balance of $11.4 million as of the Closing Date was not adjusted from its carrying amount as its fair value approximated its carrying value as of this date.

The Company acquired two operating leases and a sublease. Refer to Note 9 for additional details. The Company estimated the fair value of lease liabilities as the present value of the remaining lease payments, as if the acquired leases were new leases of the acquirer as of the Closing Date. The Company measured the right-of-use asset at the same amount as the lease liability as adjusted to reflect favorable or unfavorable terms of the lease when compared with market terms. As ACELYRIN entered into a sublease in February 2025, these sublease terms were considered at market terms. As of the Closing Date, the fair value of operating lease liabilities, current, increased by $0.2 million and the fair value of operating lease liabilities, non-current, increased by $0.5 million. As of the Closing Date, the fair value of operating lease right-of-use assets, net, decreased by $0.1 million.

Because the fair value of the identifiable assets acquired and liabilities assumed exceeded the fair value of the purchase consideration transferred, the Company recorded a gain on bargain purchase of $187.9 million as of the Closing Date. Consequently, the Company reassessed the recognition and measurement of identifiable assets acquired and liabilities assumed in accordance with ASC 805-30-25-4 and concluded that all acquired assets and assumed liabilities were recognized and that the valuation procedures and resulting measures were appropriate. Gain on bargain purchase primarily relates to the market value of ACELYRIN’s common stock trading below the carrying value of net assets and the Exchange Ratio being fixed at the time when the Merger Agreement was signed and not adjusted for subsequent changes in the market price of the Company’s common stock. Gain on bargain purchase is recognized as other income in the unaudited condensed consolidated statements of operations and comprehensive loss. The Company recognized a deferred tax liability of $10.7 million related to the acquired IPR&D intangible asset as of the Closing Date.

The Company also has additional severance related obligations under the Merger Agreement that are separate from the assets and liabilities acquired. In accordance with the ACELYRIN severance plan, ACELYRIN employees terminated without cause within 12 months of the Closing Date are entitled to receive severance benefits, including acceleration of their outstanding equity awards and extension of their outstanding options exercise periods of up to 12 months post-termination. The Company estimated total cash severance obligations, including related taxes, of $13.5 million, which it expects to pay within 12 months from the Closing Date based on agreed termination dates with employees. Severance obligation is recorded to expense over the remaining employment period for notified employees. The Company recognized $1.9 million as general and administrative expenses and $2.4 million as research and development expenses related to severance expenses for the three months ended September 30, 2025. The Company recognized $7.1 million as general and administrative expenses and $6.1 million as research and development expenses related to severance expenses for the nine months ended September 30, 2025. As of September 30, 2025, the severance liability of $1.4 million is classified as other accrued expenses and current liabilities in the unaudited condensed consolidated balance sheet. The Company estimated stock-based compensation expense of $13.1 million related to the accelerated vesting and exercise term modification for severed employees, which will be recognized during the year ending December 31, 2025. The Company recognized stock-based compensation expense of $1.0 million as general and administrative expenses and $1.1 million as research and

ALUMIS INC.

NOTES TO THE CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

(Unaudited)

development expenses for the three months ended September 30, 2025. The Company recognized stock-based compensation expense of $8.8 million as general and administrative expenses and $4.1 million as research and development expenses for the nine months ended September 30, 2025.

Following the Closing Date, the operating results of ACELYRIN have been included in the unaudited condensed consolidated financial statements. For the period from May 22, 2025 through September 30, 2025, there was no revenue attributable to ACELYRIN, and operating losses attributable to ACELYRIN for such period were $14.2 million.

The ACELYRIN Merger is intended to be a reorganization under Internal Revenue Code (“IRC”) Section 368(a). The Merger Agreement outlines the “plan of reorganization” within the meaning of the regulations issued under IRC Section 368(a) and the ACELYRIN Merger is intended to qualify as a tax-free reorganization for U.S. federal and state income tax purposes.

Unaudited Pro Forma Summary of Operations

The following table shows the unaudited pro forma summary of operations for the three and nine months ended September 30, 2025, and 2024, as if the ACELYRIN Merger had closed on January 1, 2024. The pro forma financial information is provided for comparative purposes only and is not necessarily indicative of what actual results would have been had the acquisition occurred as of January 1, 2024, nor does it give effect to synergies or any cost savings, and it is not indicative of what such results would be for any future period:


	Three Months Ended September 30,				Nine Months Ended September 30,
	2025		2024		2025		2024
Total revenue	$	2,066	$	—	$	22,121	$	—
Net income (loss)		(104,452)		(141,667)		(380,973)		(222,102)

The summary pro forma financial information includes the following adjustments:

●

actual acquisition-related transaction costs of $(0.1) million and $14.7 million were excluded from the three and nine months ended September 30, 2025 pro forma results, respectively, and zero and $14.7 million were included in the three and nine months ended September 30, 2024 pro forma results, respectively, as if these costs were incurred during the 2024 period;

●

incremental stock-based compensation expense related to the accelerated vesting and exercise term modification of $2.1 million and $12.9 million were excluded from the three and nine months ended September 30, 2025 pro forma results, respectively, and less than $0.1 million and $13.1 million were included in the three and nine months ended September 30, 2024 pro forma results, respectively, as if these costs were incurred during the 2024 period;

●

severance cash obligations for terminated ACELYRIN employees of $4.3 million and $13.2 million were excluded from the three and nine months ended September 30, 2025 pro forma results, respectively, and zero and $13.5 million were included in the three and nine months ended September 30, 2024 pro forma results, respectively, as if these costs were incurred during the 2024 period; and

●

Gain on bargain purchase of zero and $187.9 million were excluded from the three and nine months ended September 30, 2025 pro forma results, respectively, and zero and $187.9 million were included in the three and nine months ended September 30, 2024 pro forma results, respectively, as if such gains were recognized during the 2024 period.

ALUMIS INC.

NOTES TO THE CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

(Unaudited)

4.	Fair Value Measurements

The Company discloses and recognizes the fair value of its assets and liabilities using a hierarchy that prioritizes the inputs to valuation techniques used to measure fair value. The guidance establishes three levels of the fair value hierarchy as follows:

Level 1—Quoted prices in active markets for identical assets or liabilities.

Level 2—Observable inputs other than Level 1 prices, such as quoted prices for similar assets or liabilities, quoted prices in markets that are not active, or other inputs that are observable or can be corroborated by observable market data for substantially the full term of the assets or liabilities.

Level 3—Unobservable inputs that are supported by little or no market activity and that are significant to the fair value of the assets or liabilities.

Assets and liabilities measured at fair value are classified in their entirety based on the lowest level of input that is significant to the fair value measurement. The Company’s assessment of the significance of a particular input to the fair value measurement in its entirety requires management to make judgments and consider factors specific to the asset or liability. The Company recognizes transfers into and out of levels within the fair value hierarchy in the period in which the actual event or change in circumstances that caused the transfer occurs.

The Company’s financial instruments consist of Level 1, Level 2 and Level 3 financial instruments. Changes in the ability to observe valuation inputs may result in a reclassification of levels of certain securities within the fair value hierarchy.

Level 1 financial instruments are comprised of money market funds and U.S. Treasury obligations. Level 2 financial instruments are comprised of U.S. Treasury obligations, corporate debt obligations, commercial paper, supranational debt obligations and government development bank obligations. Short term marketable securities are considered Level 2 when their fair values are determined using inputs that are observable in the market or can be derived principally from or corroborated by observable market data such as pricing for similar securities, recently executed transactions, cash flow models with yield curves, and benchmark securities. In addition, Level 2 financial instruments are valued using comparisons to like-kind financial instruments and models that use readily observable market data as their basis. Level 3 financial instruments include derivative liabilities issued in March 2024 and settled in May 2024 in connection with the closing of the second tranche of the Series C redeemable convertible preferred stock financing.

ALUMIS INC.

NOTES TO THE CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

(Unaudited)

The following tables present the Company’s fair value hierarchy for financial assets measured at fair value on a recurring basis as of September 30, 2025 and December 31, 2024 (in thousands):


	September 30, 2025
	Level 1		Level 2		Level 3		Total
Assets:
Cash equivalents
Money market funds	$	61,174	$	—	$	—	$	61,174
Marketable securities
U.S. Treasury obligations		173,331		64,576		—		237,907
Corporate debt obligations		—		38,049		—		38,049
Commercial paper		—		22,535		—		22,535
Supranational debt obligations		—		9,963		—		9,963
Government development bank obligations		—		4,013		—		4,013
Total assets	$	234,505	$	139,136	$	—	$	373,641


	December 31, 2024
	Level 1		Level 2		Level 3		Total
Assets:
Cash equivalents
Money market funds	$	168,847	$	—	$	—	$	168,847
Marketable securities
U.S. Treasury obligations		47,137		71,600		—		118,737
Total assets	$	215,984	$	71,600	$	—	$	287,584

In connection with the Series C redeemable convertible preferred stock financing in March 2024, the Company issued to investors two freestanding financial instruments: the Series C second tranche option liability and the put right option liability. The Company estimated their fair value using a Black-Scholes option pricing model weighted by the probability of occurring. The Company used the intrinsic value calculation to estimate the fair value of the Series C second tranche option liability and the put right option liability upon settlement. Significant estimates and assumptions impacting the derivative liability fair value included the probability of each option exercise, redeemable convertible preferred stock fair value, estimated stock volatility and the expected term.

The following table provides a range of assumptions used in the valuation of the derivative liabilities for the nine months ended September 30, 2024:


	Nine Months Ended September 30,
		2024
Expected term (in years)		0.2 – 0.4
Volatility		55.1% – 59.9%
Risk-free interest rate		5.4% – 5.5%
Dividend yield		0.00%
Probability of option exercise		0.0% – 100.0%

The following table provides a roll-forward of the fair value of the Company’s Level 3 financial instrument, the derivative liabilities, for the nine months ended September 30, 2024 (in thousands):

ALUMIS INC.

NOTES TO THE CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

(Unaudited)


	Nine Months Ended September 30,
	2024
Fair value at beginning of period	$	—
Fair value upon issuance		8,913
Changes in fair value		5,406
Fair value upon settlement		(14,319)
Fair value at end of period	$	—

The Company did not hold Level 3 financial instruments for the three and nine months ended September 30, 2025. There were no transfers between Level 1, Level 2 or Level 3 categories for the nine months ended September 30, 2025 and 2024.

5.	Marketable Securities

Marketable securities, which are classified as available-for-sale marketable securities, consisted of the following as of September 30, 2025 and December 31, 2024 (in thousands):


	September 30, 2025
			Gross		Gross
	Amortized Cost		Unrealized		Unrealized		Fair
	Basis		Gains		Losses		Value
Short-term marketable securities:
U.S. Treasury obligations	$	237,785	$	123	$	(1)	$	237,907
Corporate debt obligations		38,024		27		(2)		38,049
Commercial paper		22,517		18		—		22,535
Supranational debt obligations		9,956		7		—		9,963
Government development bank obligations		4,009		4		—		4,013
Total short-term marketable securities	$	312,291	$	179	$	(3)	$	312,467


	December 31, 2024
			Gross		Gross
	Amortized Cost		Unrealized		Unrealized		Fair
	Basis		Gains		Losses		Value
Short-term marketable securities:
U.S. Treasury obligations	$	118,697	$	45	$	(5)	$	118,737
Total short-term marketable securities	$	118,697	$	45	$	(5)	$	118,737

All marketable securities held as of September 30, 2025 and December 31, 2024 had contractual maturities of less than one year.

As of September 30, 2025 and December 31, 2024, no significant facts or circumstances were present to indicate a deterioration in the creditworthiness of the issuers of the marketable securities, and the Company has no requirement or intention to sell these securities before maturity or recovery of their amortized cost basis. The Company considered the current and expected future economic and market conditions and determined that its marketable securities were not significantly impacted. For all marketable securities with a fair value less than its amortized cost basis, the Company determined the decline in fair value below amortized cost basis to be immaterial and non-credit related, and therefore no allowance for expected credit losses was recorded for the three and nine months ended September 30, 2025 and 2024.

ALUMIS INC.

NOTES TO THE CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

(Unaudited)

6.Balance Sheet Components

Restricted Cash

Restricted cash includes cash held at financial institutions that is pledged as collateral for stand-by letters of credit, of $1.4 million and $1.1 million related to lease commitments as of September 30, 2025 and December 31, 2024, respectively. The cash will be restricted until the termination or modification of the related lease agreements. Restricted cash is classified as restricted cash, non-current in the condensed consolidated balance sheets as of September 30, 2025 and December 31, 2024.

Other Prepaid Expenses and Current Assets

Other prepaid expenses and current assets consisted of the following as of September 30, 2025 and December 31, 2024 (in thousands):


	September 30,		December 31,
	2025		2024
Prepaid credit voucher for clinical manufacturing	$	3,222	$	—
Interest receivable		1,987		698
Prepaid subscriptions		1,657		1,232
Tax receivable		1,650		1,114
Prepaid insurance		1,094		695
Other		1,001		762
Total other prepaid expenses and current assets	$	10,611	$	4,501

The prepaid credit voucher for clinical manufacturing was received by ACELYRIN in the third quarter of 2024 as part of an agreement to cancel certain services with a vendor under a manufacturing agreement related to the suspension of development of certain ACELYRIN programs. The prepaid credit voucher for clinical manufacturing may be used to settle invoices for services and raw materials from this vendor related to the lonigutamab product candidate in development by ACELYRIN. As of September 30, 2025, the prepaid credit voucher for clinical manufacturing included $3.2 million classified in other prepaid expenses and current assets and $5.2 million included in other assets, non-current.

Property and Equipment, Net

Property and equipment, net consisted of the following as of September 30, 2025 and December 31, 2024 (in thousands):


	Estimated Useful Life	September 30,		December 31,
	(in years)	2025		2024
Leasehold improvements	Shorter of useful life or lease term	$	17,655	$	17,618
Laboratory equipment	5		5,844		5,227
Furniture and fixtures	5		1,709		1,709
Computer equipment	5		896		896
Capitalized software	3		75		75
Total property and equipment, gross			26,179		25,525
Less: Accumulated depreciation and amortization			(7,121)		(4,557)
Total property and equipment, net		$	19,058	$	20,968

Depreciation and amortization expense was $0.9 million and $0.8 million for the three months ended September 30, 2025 and 2024, respectively, and $2.6 million and $2.3 million for the nine months ended September 30, 2025 and 2024, respectively.

ALUMIS INC.

NOTES TO THE CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

(Unaudited)

Other Accrued Expenses and Current Liabilities

Other accrued expenses and current liabilities consisted of the following as of September 30, 2025 and December 31, 2024 (in thousands):


	September 30,		December 31,
	2025		2024
Accrued personnel and related expenses	$	12,167	$	7,765
Accrued professional services and other		5,217		2,657
Severance liability		1,374		—
Accrued other expenses		63		158
Total other accrued expenses and current liabilities	$	18,821	$	10,580

Revenue

Kaken Collaboration Agreement

On March 25, 2025, (the “Effective Date”) the Company entered into a collaboration and license agreement (the “Collaboration Agreement”) with Kaken Pharmaceutical Co., Ltd. (“Kaken”). Under the terms of the Collaboration Agreement, the Company granted to Kaken an exclusive right to develop, manufacture and commercialize envudeucitinib (or “envu”), formerly known as ESK-001, for dermatology indications in Japan, with options to expand the license, subject to opt-in payments and certain cost-sharing obligations on the part of Kaken, to include rheumatological and gastrointestinal diseases.

Pursuant to the terms of the Collaboration Agreement, the Company is responsible for the global development of envu in the dermatology field, and Kaken is responsible for the clinical development, regulatory approvals and commercialization of envu in Japan in dermatology and other indications for which Kaken has exercised its option. Kaken is required to use commercially reasonable efforts to conduct all subsequent development, manufacture, and commercialization activities. The Collaboration Agreement further provides that the Company will retain rights to envu in all other indications and geographies.

In March 2025, Kaken made an upfront, non-refundable payment of $20.0 million to the Company. In addition, Kaken will pay the Company an aggregate of $20.0 million towards global development costs for envu in the dermatology field through the end of 2026 and thereafter will pay a specified share of development costs applicable to the dermatology field, and for any field for which Kaken exercises its option, subject to Kaken's right to opt out of cost-sharing in certain indications in specified circumstances. In addition, Kaken would pay the Company up to an aggregate of $36.0 million upon the achievement of regulatory milestones and upon Kaken’s exercise of its field expansion options for the rheumatology and gastrointestinal fields. In addition, the Company is entitled to receive aggregate payments of up to ¥15.5 billion upon the achievement of commercial milestones, plus tiered royalties at percentages ranging from the low double digits into the twenties on aggregate net sales of envu in Japan.

The Company evaluated the Collaboration Agreement and concluded it was within the scope of ASC 606. As of the Effective Date, the Company identified four performance obligations: (1) license to develop, manufacture and commercialize envu (the “License Obligation”), (2) development services that support the global development of envu (the “Development Services Obligation”), (3) the manufacture of the clinical supply in Japan (the “Manufacturing Services Obligation”) and (4) a material right related to the option for rheumatology disease (the “Material Right Obligation”). The License Obligation was considered functional intellectual property and distinct from other promises under the contract, as Kaken can benefit from the license on its own or together with other readily available resources. The Development Services Obligation and Manufacturing Services Obligation were considered distinct as Kaken could benefit from both of these separately with the license transferred by the Company at the inception of the agreement. The option in the rheumatology field contained a material right because its exercise does not require payment of a fee that is commensurate with the value

ALUMIS INC.

NOTES TO THE CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

(Unaudited)

of the additional license. No material right was assigned to the gastrointestinal field since its estimated fair value did not exceed the exercise price of the option.

The transaction price includes the upfront license fee of $20.0 million, the global development cost reimbursement of $20.0 million in the dermatology field through the end of 2026, the estimated global development cost reimbursement in the dermatology field after 2026 of $1.5 million and an immaterial amount of variable consideration related to the Manufacturing Services Obligation. The Company determined that any variable consideration related to development and regulatory milestones was deemed to be fully constrained at inception and therefore excluded from the initial transaction price due to the high degree of uncertainty and risk associated with these potential payments, and the Company could not assert that it was probable that a significant reversal in the amount of cumulative revenue recognized would not occur.

The Company developed the estimated standalone selling prices for the License Obligation and Material Right Obligation primarily based on the probability-weighted value of expected future revenues associated with each underlying license. In developing such estimates, the Company applied judgment in determining the forecasted revenue, taking into consideration the applicable market conditions, the probability of success, and the time needed to develop each indication for which the license relates. The Company developed the estimated standalone selling price for the development services and clinical supply primarily based on the resources to be committed to perform the service.

At inception of the contract, the Company allocated $17.4 million to the License Obligation, $20.8 million to the Development Services Obligation, $3.3 million to the Material Right Obligation and an immaterial amount to the Manufacturing Services Obligation. The License Obligation was satisfied in March 2025 upon transfer of the license to Kaken. For the Development Services Obligation, the Company recognizes revenue over time as Kaken consumes the benefit of such services as they are being performed. The Company measures proportional performance over time for the Development Services Obligation by using an input method based on cost incurred relative to the total estimated cost of the obligation on a quarterly basis. The Company re-evaluates the transaction price as uncertain events are resolved or other changes in circumstances occur as of the end of each reporting period.

The Company recognized revenue of zero and $17.4 million for the three and nine months ended September 30, 2025, respectively, related to the License Obligation and $2.1 million and $4.7 million for the three and nine months ended September 30, 2025, respectively, related to the Development Services Obligation and Manufacturing Services Obligation. As of September 30, 2025, collaboration revenue receivable was less than $0.1 million, and deferred revenue, non-current was $1.9 million. The aggregate estimated amount of transaction price that was unsatisfied as of September 30, 2025 was $19.4 million, of which, $16.2 million related to the Development Services Obligation that is expected to be recognized through 2028 as the Company performs its services towards the global development of envu in the dermatology field. The remaining $3.3 million estimated amount of transaction price that was unsatisfied as of September 30, 2025 related to the Material Right Obligation and is deferred until the option is exercised or expires.

Tenet Medicines Purchase Agreement

In January 2024, ACELYRIN entered into an asset purchase agreement (“Purchase Agreement”) with Tenet Medicines, Inc. (“Tenet”). In consideration for the assets and other rights Tenet received under the Purchase Agreement, ACELYRIN is entitled to receive development, regulatory and commercial milestone payments of up to $157.5 million in the aggregate based on the achievement of specified milestones, royalties on worldwide net sales and payments on sublicense income.

ALUMIS INC.

NOTES TO THE CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

(Unaudited)

8.	Related Party Transactions

Foresite Labs Services Agreement

Foresite Labs, LLC (“Foresite Labs”) is an affiliate of Foresite Capital Management, a stockholder of the Company. In January 2021, the Company entered into a services agreement with Foresite Labs, which was amended and restated in August 2021 and in December 2023, and expires in December 2026, unless terminated earlier by the parties. Thereafter, on each anniversary of the effective date, the agreement will automatically renew for an additional one-year term, unless terminated earlier by the parties. Foresite Labs provides services to assist the Company in exploring specified immunology genetic targets. For the three months ended September 30, 2025 and 2024, the Company recognized $0.3 million and $0.2 million as research and development expenses under the service agreement, respectively. For the nine months ended September 30, 2025 and 2024, the Company recognized $0.8 million and $0.7 million as research and development expenses under the services agreement, respectively. Accrued expenses under the service agreement were zero as of September 30, 2025 and December 31, 2024.

9.Commitments and Contingent Liabilities

Operating Leases

In August 2022, the Company entered into a lease agreement for 55,000 square feet of office and laboratory space in South San Francisco, California, which commenced in January 2023 and has a contractual termination date in August 2033. The Company constructed leasehold improvements in the space, which were concluded to be lessee assets. The lessor provided the Company a tenant improvement allowance of $17.2 million, of which $0.5 million was received in the year ended December 31, 2022, and $16.7 million was received in the year ended December 31, 2023, and was accounted for as a reduction to lease payments. At the commencement date, future lease payments totaled $37.9 million, including $54.6 million in gross fixed payments, less $16.7 million in lease incentives expected to be received during the first year of the lease. The lease liability at lease commencement was calculated to be $14.1 million, which is equal to the present value of the future lease payments, discounted at an incremental borrowing rate of 11.4%. Following the commencement date, the Company measured its lease liability and right-of-use asset in accordance with ASC 842-20-35-3. In accordance with this guidance, future lease payments increased as the $16.7 million incentive was received and future gross fixed payments were no longer offset by these incentives. Leasehold improvements were reflected in property and equipment, net in the condensed consolidated balance sheets as of September 30, 2025 and December 31, 2024. The lease agreement also includes a renewal option allowing the Company to extend this lease for an additional three years at the prevailing rental rate, which the Company was not reasonably certain to exercise.

In December 2024, the Company entered into a lease agreement for approximately 22,000 square feet of additional office space in South San Francisco, California. The lease has a contractual termination date of December 2026, with the right to extend the lease for an additional two years subject to certain conditions. The Company determined that, for accounting purposes, the commencement date of the lease is in January 2025 and the lease term ends in December 2026, as it was not reasonably certain that the lease would be extended. As of the commencement date, future lease payments totaled $1.9 million and the lease liability was calculated to be $1.8 million, which is equal to the present value of the future lease payments, discounted at an incremental borrowing rate of 7.9%.

Upon the closing of the ACELYRIN Merger, the Company became the successor to ACELYRIN’s rights under ACELYRIN’s lease and sublease agreements. In January 2023, ACELYRIN entered into a lease agreement to rent approximately 10,012 square feet of office space in Southern California. The term of the lease is 65 months with an option to extend it for an additional three years. Monthly rent payments are approximately $30,500, subject to an annual 3.0% increase. In addition to the base rent, the Company is obligated to pay variable costs related to its share of operating expenses and taxes.

ALUMIS INC.

NOTES TO THE CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

(Unaudited)

In July 2023, ACELYRIN entered into a lease agreement to rent approximately 22,365 square feet of office space in South San Francisco, California. The term of the lease is 60 months with an option to extend it for an additional five years. Monthly base rent payments are approximately $150,000, subject to an annual 3.5% increase. In addition to the base rent, the Company is obligated to pay variable costs related to its share of operating expenses and taxes. In February 2025, ACELYRIN entered into an agreement to sublease the entirety of its South San Francisco leased space through October 2029, the remainder of the lease term. The sublease included the operating lease right-of-use asset and certain property, plant and equipment. Sublease income was immaterial for the three and nine months ended September 30, 2025.

The components of lease costs were as follows (in thousands):


	Three Months Ended September 30,				Nine Months Ended September 30,
	2025		2024		2025		2024
Operating lease costs	$	1,377	$	882	$	3,682	$	2,593
Variable lease costs		336		297		993		953
Total lease costs	$	1,713	$	1,179	$	4,675	$	3,546

Supplemental cash flow information related to the operating leases was as follows (in thousands):

Weighted-average remaining lease term and incremental borrowing rate for the operating leases were as follows:


	September 30,		December 31,
	2025		2024
Weighted-average remaining lease term (years)	7.0		8.7
Weighted-average incremental borrowing rate	11.6	%	11.4	%

Future minimum lease payments under non-cancelable leases as of September 30, 2025, were as detailed below (in thousands):


2025 (remainder of the year)	$	2,229
2026		8,175
2027		7,648
2028		7,765
2029		7,205
Thereafter		21,857
Total undiscounted lease payments		54,879
Less: Imputed interest		(17,082)
Total operating lease liabilities	$	37,797

FronThera Contingent Consideration

In March 2021, the Company entered into a stock purchase agreement to acquire FronThera U.S. Holdings, Inc. and its wholly owned subsidiary, FronThera U.S. Pharmaceuticals LLC. (the “FronThera Acquisition”), and the transaction was accounted for as an asset acquisition. Under the stock purchase agreement, the Company is obligated to pay contingent consideration of up to an aggregate of $120.0 million based on the achievement of specified clinical and approval milestones, of up to an aggregate of $70.0 million payable for clinical milestones, and of up to an aggregate of $50.0 million payable for approval milestones, all related to technology acquired under the agreement. In the year ended

ALUMIS INC.

NOTES TO THE CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

(Unaudited)

December 31, 2022, the Company incurred and made a $37.0 million milestone payment for the first administration of envu to a patient enrolled in a Phase 2 clinical trial of envu, which was recorded in research and development expenses in the consolidated statement of operations and comprehensive loss. In July 2024, the Company met a milestone in connection with the first administration of envu to a patient enrolled in a Phase 3 clinical trial of envu and made a $23.0 million milestone payment in August 2024, which was recorded in research and development expenses in the consolidated statement of operations and comprehensive loss for year ended December 31, 2024. No other milestones were achieved or were probable of being achieved as of September 30, 2025.

License and Commercialization Agreement with Pierre Fabre

Upon the closing of the ACELYRIN Merger, the Company became the successor to ACELYRIN’s rights under the March 25, 2021 license and commercialization agreement with Pierre Fabre Medicament SAS (“Pierre Fabre”), as amended (the “Pierre Fabre Agreement”), through which ACELYRIN received certain exclusive worldwide licenses with the right to sublicense certain patents, know-how and other intellectual property to develop, manufacture, use and commercialize lonigutamab for non-oncology therapeutic indications. The license from Pierre Fabre extends to any product containing lonigutamab (excluding any fragments or derivatives) as its sole active ingredient (each, a “PF Licensed Product”). The Pierre Fabre Agreement prohibits the Company from using the licensed intellectual property in any antibody drug conjugate, multi-specific antibodies or any other derivatives of lonigutamab.

The Company is obligated to (i) make payments of up to $100.5 million upon the achievement of various development and regulatory milestones, (ii) make milestone payments of up to $390.0 million upon the achievement of certain commercial milestones, and (iii) pay tiered royalties in the high single-digit to low-teen percentages to Pierre Fabre on worldwide net sales in a given calendar year. Royalties will be payable for each PF Licensed Product in a given country during a period commencing upon the first commercial sale of such PF Licensed Product in such country and continuing until the latest of (a) 10 years after such first commercial sale, (b) expiration of last-to-expire valid claim in a licensed patent in such country and (c) expiration of regulatory exclusivity for such PF Licensed Product in such country. In the event the Company enters into a sublicense with a third party, the Company must also share with Pierre Fabre a percentage of any revenues from option fees, upfront payments, license maintenance fees, milestone payments or the like generated from the sublicense. Such percentage may be between the high single-digits to the low thirties based on which stage of development of a PF Licensed Product the sublicense relates to.

Unless earlier terminated, the Pierre Fabre Agreement will continue on a PF Licensed Product-by-PF Licensed Product and country-by-country basis until there are no more royalty payments owed to Pierre Fabre on any PF Licensed Product thereunder. Either party may terminate the Pierre Fabre Agreement upon an uncured material breach, or upon the bankruptcy or insolvency of the other party. Pierre Fabre may also terminate the agreement if the Company or any of its affiliates institutes a patent challenge against the licensed patents from Pierre Fabre. The Company may also terminate the Pierre Fabre Agreement with or without cause upon nine months’ prior written notice, so long as there is no ongoing clinical trial for any PF Licensed Product.

As of September 30, 2025, no milestones were probable and accrued in the unaudited condensed consolidated balance sheets.

Purchase Commitments

The Company enters into various agreements in the ordinary course of business, such as those with suppliers, clinical research organizations (“CROs”), contract manufacturing organizations (“CMOs”) and clinical trial sites. Upon the closing of the ACELYRIN Merger, the Company became the successor to contracts with non-cancellable commitments under ACELYRIN contracts. As of September 30, 2025, and December 31, 2024, the total value of non-cancellable purchase commitments under contracts was $4.4 million and zero, respectively. This presentation of non-cancellable purchase commitments does not include any estimates of potential reduction of such liabilities related to mitigation obligations of the counterparties in the event of cancellation under the terms of its engagements.

ALUMIS INC.

NOTES TO THE CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

(Unaudited)

Legal Contingencies

From time to time, the Company has and may become involved in legal proceedings arising in the ordinary course of business, any or all of which could have a material adverse impact on the Company, including its financial position. The outcomes of legal proceedings are not within the Company’s complete control and may not be known for prolonged periods of time. The Company records a liability for such matters when it is probable that future losses will be incurred and that such losses can be reasonably estimated. Significant judgment by the Company is required to determine both probability and the estimated amount.

On November 15, 2023, a purported federal securities class action lawsuit was commenced in the United States District Court for the Central District of California. On February 15, 2024, the Court appointed joint lead plaintiffs and lead counsel. An amended complaint was filed on March 26, 2024 (Boukadoum v. Acelyrin, Inc. et al., No. 2:23-cv-09672-FMO-MAA), naming ACELYRIN and then-current and former executive officers and directors as defendants. The complaint alleges that the defendants violated the Exchange Act and Securities Act by misleading investors about the Phase 2b trial of izokibep in hidradenitis suppurativa. The original complaint was filed following ACELYRIN’s announcement of the week 16 results from the Part B portion of such Phase 2b trial. The amended complaint seeks damages and an award of reasonable costs and expenses, including attorneys’ fees, expert fees and other costs, as well as such other and further relief as the court may deem just and proper. On May 3, 2024, defendants filed their motion to dismiss the amended complaint, which remains pending.

It is possible that additional suits will be filed, or allegations made by stockholders, with respect to these same or other matters and also naming the Company and/or its officers and directors as defendants. This lawsuit and any other potential lawsuits are subject to inherent uncertainties, and the actual defense and disposition costs will depend upon many unknown factors. The outcome of this lawsuit is necessarily uncertain. The Company could be forced to expend significant resources in the defense against this and any other related lawsuits and the Company may not prevail. The Company currently is not able to estimate the possible loss to the Company from this lawsuit, as this lawsuit is currently at an early stage, and such amounts could be material to the Company’s financial statements even if the Company prevails in the defense against this lawsuit. The Company cannot be certain how long it may take to resolve this lawsuit or the possible amount of any damages that the Company may be required to pay. As of September 30, 2025, the Company does not consider any payment to be probable or reasonably estimable and has not accrued for any potential liability relating to this lawsuit.

Guarantees and Indemnifications

In the normal course of business, the Company enters into agreements that contain a variety of representations and provide for general indemnification. Its exposure under these agreements is unknown because it involves claims that may be made against the Company in the future. To the extent permitted under Delaware law, the Company has agreed to indemnify its directors and officers for certain events or occurrences while the director or officer is, or was serving, at a request in such capacity. To date, the Company has not paid any claims or been required to defend any action related to its indemnification obligations. As of September 30, 2025 and December 31, 2024, the Company did not have any material indemnification claims that were probable or reasonably possible and consequently has not recorded related liabilities.

10.	Redeemable Convertible Preferred Stock

In March 2024, the Company issued and sold an aggregate of 41,264,891 shares of Series C redeemable convertible preferred stock for gross proceeds of $129.5 million and incurred $0.4 million of offering costs. The purchase price for Series C redeemable convertible preferred stock was $3.13826 per share. Under the Series C stock purchase agreement, any time prior to the earliest of (i) December 31, 2024, (ii) the execution of a letter of intent for the sale of the Company, or (iii) the closing date of the Company’s IPO, at the discretion of the Company’s board of directors, the Company was obligated to sell and each Series C purchaser was obligated to purchase additional shares of Series C redeemable convertible preferred stock with the amount equal to the purchaser’s aggregate purchase price in the first tranche Series C closing less any previous payments by the purchaser as part of the Put Right (as defined below) exercise. If the purchaser

ALUMIS INC.

NOTES TO THE CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

(Unaudited)

did not purchase its full share in the second tranche closing (the “Second Tranche Series C Closing”), all of its existing shares of Series C redeemable convertible stock and Series C-1 redeemable convertible preferred stock were convertible into voting common stock at a 10-to-1 basis. Additionally, a purchaser had a right to purchase shares of Series C-1 redeemable convertible preferred stock at a purchase price of $4.00 per share beginning from the earlier of (a) September 4, 2024 or (b) the date of a significant partnering or collaboration agreement and expiring upon the earlier of (a) December 31, 2024, (b) the public filing of a registration statement on Form S-1 for the IPO, (c) the Second Tranche Series C Closing and (d) the execution of a letter of intent for the sale of the Company (the “Put Right”). The Put Right could only be exercised once. The Company determined that the Second Tranche Series C Closing and the Put Right were two freestanding financial instruments and recognized the derivative liabilities at their estimated fair value of $8.9 million at the issuance date.

In May 2024, the Company closed the Second Tranche Series C Closing and issued an additional 41,264,892 shares of Series C redeemable convertible preferred stock at a price of $3.13826 per share. The Company received gross proceeds of $129.5 million and incurred $0.2 million of offering costs. Accordingly, the derivative liabilities were settled, and the Company reclassified the derivative liabilities, remeasured at fair value of $14.3 million, into redeemable convertible preferred stock.

Immediately prior to the closing of the Company’s IPO on July 1, 2024, all outstanding shares of the Company’s redeemable convertible preferred stock were converted and then redesignated into voting and non-voting common stock and are no longer outstanding.

11.	Stockholders’ Equity

As of September 30, 2025, the Company was authorized to issue 50,000,000 shares of preferred stock, 492,815,092 shares of voting common stock and 7,184,908 shares of non-voting common stock, all with par values of $0.0001 per share. As of September 30, 2025, there were no shares of preferred stock issued or outstanding, 97,174,231 shares of voting common stock issued and outstanding and 7,184,908 shares of non-voting common stock issued and outstanding.

The holders of voting and non-voting common stock have the same rights except that non-voting common stock does not have voting rights, except as may be required by law. Each holder of non-voting common stock has a right to convert each share of non-voting common stock to one share of voting common stock subject to the following limitations. At any time following the Company’s registration of any class of equity securities under the Exchange Act, the holders of shares of non-voting common stock may not convert a number of shares of non-voting common stock into shares of voting common stock in excess of that number of shares of non-voting common stock which would cause the holder thereof to beneficially own (for purposes of Section 13(d) of the Exchange Act), in excess of 4.99% of the total number of issued and outstanding shares of voting common stock. Such maximum percentage may be increased or decreased to such other percentage as any holder of outstanding shares of non-voting common stock may designate in writing (in the case of an increase upon 61 days’ prior written notice).

ALUMIS INC.

NOTES TO THE CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

(Unaudited)

Common stock reserved for issuance, on an as-converted basis, consisted of the following as of September 30, 2025 and December 31, 2024:


	September 30,	December 31,
	2025	2024
Stock options issued and outstanding	20,090,359	9,458,788
RSUs issued and outstanding	2,670,905	—
Shares available for grant under the 2024 Equity Incentive Plan	930,301	6,893,517
Shares available for grant under the 2024 Employee Stock Purchase Plan	1,009,440	650,000
Shares available for grant under the ACELYRIN, Inc. 2023 Equity Incentive Plan	6,448,105	—
Shares available for grant under the 2024 Performance Option Plan	199,856	92,800
Total	31,348,966	17,095,105

Common Stock Issued to Executives

In February 2021, the Company issued 100,532 shares of restricted common stock to two executives at a purchase price of $0.94 per share. The shares vested over a four-year period with a one-year cliff. While the shares were unvested, the holders had voting and dividends rights and the Company had the right to repurchase unvested shares of common stock at the price paid by the holder in the event of termination of the holder’s continuous status as a service provider. The Company estimated the fair value of the restricted stock awards based on the fair value of common stock at the grant dates. The expense was recognized ratably over the vesting terms. The Company recognized less than $0.1 million of stock-based compensation expense for the three and nine months ended September 30, 2025 and 2024.

The following table summarizes the activity for the Company’s restricted common stock for the nine months ended September 30, 2025:


		Weighted-
		Average
	Number of	Grant Date
	Shares	Fair Value
Unvested as of December 31, 2024	2,583	$	2.90
Vested	(2,583)	$	2.90
Unvested as of September 30, 2025	—	$	—

12.	Stock-Based Compensation

2021 Stock Plan

In February 2021, the Company adopted its 2021 Stock Plan (the “2021 Plan”), which provided for stock awards to eligible employees, directors and consultants of the Company. Awards issuable under the 2021 Plan included incentive stock options (“ISOs”), non-statutory stock options (“NSOs”), RSUs and stock grants. Subsequent to the adoption of the 2024 Equity Incentive Plan (the “2024 EIP”) in June 2024, described below, no additional shares were available for issuance under the 2021 Plan, and any stock options granted under the 2021 Plan that were subsequently forfeited would be made available for issuance under the 2024 EIP.

The terms of the 2021 Plan permit option holders to exercise options before their options are vested. The shares of common stock granted upon early exercise that have not yet vested are subject to repurchase by the Company in the event of termination of the holder’s continuous status as a service provider, at the price paid by the holder.

ALUMIS INC.

NOTES TO THE CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

(Unaudited)

Stock Option Repricing

In March 2024, the Company’s board of directors approved the repricing of all outstanding options as of March 29, 2024, which have an exercise price exceeding $8.84 per share. The exercise price of outstanding options with a weighted average exercise price of $10.23 for 4,603,443 common stock shares was reduced to the estimated common stock fair value of $8.84 per share at the date of the repricing. The vesting terms and expiration dates remain unchanged from the original grant dates.

The stock option repricing was treated as an option modification for accounting purposes and resulted in total incremental expense of $0.7 million, of which $0.1 million incremental expense associated with the vested options was recognized on the modification date. The remaining $0.6 million incremental expense associated with the unvested options as of the modification date is being recognized over the remainder of the original requisite service period.

2024 Performance Option Plan

In May 2024, the Company’s board of directors adopted, and its stockholders approved, the 2024 Performance Option Plan (the “2024 POP”). The Company reserved 1,880,680 shares of common stock issuable under the 2024 POP. The 2024 POP permits grants of ISOs, NSOs and restricted stock awards to the Company’s employees, directors and consultants.

In May 2024, the Company granted NSOs to employees to purchase 1,880,680 shares of common stock at an exercise price of $10.19 under the 2024 POP. Options generally vest on the date when the Company meets certain common stock public market price specified targets after the end of the IPO lock-up period, subject to continuous service through each respective vest date. The price targets are calculated based on the volume weighted average price per share over 30 consecutive trading dates, in accordance with the grant terms. The unvested awards will expire if it is determined that the vesting conditions have not been met during the applicable six-year performance period. The service condition includes monthly vesting over 36 months from the vesting commencement date and the employee’s continuous service with the Company through each such monthly vesting date. The terms of the 2024 POP permit option holders to exercise options before their options are vested if the market condition has been met.

2024 Equity Incentive Plan

In June 2024, the Company’s board of directors adopted, and its stockholders approved, the 2024 EIP, which became effective on June 27, 2024, upon execution of the underwriting agreement related to the Company’s IPO. The Company reserved 7,800,000 new shares of common stock for issuance under the 2024 EIP. In addition, up to 6,829,339 shares subject to awards under the 2021 Plan that terminate, expire, or lapse for any reason without the delivery of shares, or are reacquired or withheld (or not issued) to satisfy a tax withholding obligation or the purchase or exercise price, were authorized to be added to the 2024 EIP. The 2024 EIP is a successor to the 2021 Plan and no further grants will be made under the 2021 Plan. The 2024 EIP also provides that the number of shares initially reserved and available for issuance will automatically increase each January 1, beginning on January 1, 2025 through January 1, 2034, by an amount equal to 5% of the outstanding number of shares of the Company’s common stock as of the last day of the immediately preceding fiscal year, or such lesser number of shares as determined by the board of directors prior to the applicable January 1. Pursuant to this evergreen provision, the Company increased the number of shares reserved under the 2024 EIP by 2,720,366 on January 1, 2025. No more than 43,888,017 shares of common stock may be issued upon the exercise of incentive stock options under the 2024 EIP.

The 2024 EIP allows the Company to make equity-based awards to its officers, employees, directors and consultants. The 2024 EIP provides for the grant of ISOs, NSOs, restricted stock awards, RSUs, stock appreciation rights, performance awards and other stock-based awards. Options under the 2024 EIP may be granted for periods of up to 10 years at exercise prices no less than the fair market value of common stock on the date of grant; provided, however, that the exercise price of an incentive stock option granted to a 10% stockholder may not be less than 110% of the fair market value of the shares on the date of grant and such option may not be exercisable after the expiration of five years from the date of grant. Stock

ALUMIS INC.

NOTES TO THE CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

(Unaudited)

option grants under the 2024 EIP generally vest over four years. The grant date fair market value of all awards made under the 2024 EIP and all cash compensation paid by the Company to any non-employee director for services as a director in any fiscal year may not exceed $750,000, increased to $1,000,000 in the fiscal year of their initial service as a non-employee director. The terms of the 2024 EIP do not permit option holders to exercise options before their options are vested.

ACELYRIN Plans

Pursuant to the Merger Agreement, the Company assumed certain stock options, RSUs and performance RSUs outstanding under the ACELYRIN, Inc. 2020 Stock Option and Grant Plan, as amended (the “ACELYRIN 2020 Plan”), the ValenzaBio, Inc. Stock Plan (the “ValenzaBio Plan”) and the ACELYRIN, Inc. 2023 Equity Incentive Plan (the “ACELYRIN 2023 Plan” and, together with the ACELYRIN 2020 Plan and the ValenzaBio Plan, the “ACELYRIN Plans”). In connection with the closing of the ACELYRIN Merger, the Company also assumed the ACELYRIN 2023 Plan, which, as modified in connection with such assumption, permits equity awards to be issued to the extent permissible under applicable law and Nasdaq listing rules.

Stock options that were outstanding under the ACELYRIN Plans immediately prior to the Closing Date were assumed by the Company and converted into options to purchase the Company’s common stock. RSUs that were outstanding and unvested immediately prior to the Closing Date were assumed by the Company and converted into the Company’s RSU awards. Performance RSUs outstanding and unvested immediately prior to the Closing Date were converted into the Company’s RSU awards subject only to a service vesting condition.

Stock Option Activity

The following table summarizes the Company’s stock option activity, excluding under the 2024 POP, for the nine months ended September 30, 2025 and includes early exercised shares as part of options exercised:


				Weighted-
		Weighted-		Average
		Average		Remaining	Aggregate
		Exercise		Contractual	Intrinsic
		Price Per		Term	Value
	Options	Share		(in years)	(in thousands)
Outstanding as of December 31, 2024	7,670,908	$	9.59	8.2	$	1,777
Stock options assumed in connection with the ACELYRIN Merger	4,712,186	$	12.99
Granted	6,983,120	$	4.60
Exercised	—	$	—		$	—
Forfeited or expired	(956,679)	$	9.07
Outstanding, vested and expected to vest as of September 30, 2025	18,409,535	$	8.60	7.0	$	388
Exercisable as of September 30, 2025	10,661,758	$	10.66	5.2	$	116

Total exercisable shares of 10,661,758 as of September 30, 2025 included 2,304,921 unvested shares that were early exercisable under the 2021 Plan. The total fair value of stock options vested during the nine months ended September 30, 2025 and 2024 was $22.1 million and $5.4 million, respectively.

ALUMIS INC.

NOTES TO THE CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

(Unaudited)

The following table summarizes the Company’s stock option activity under the 2024 POP for the nine months ended September 30, 2025:


				Weighted-
		Weighted-		Average
		Average		Remaining		Aggregate
		Exercise		Contractual		Intrinsic
		Price Per		Term		Value
	Options	Share		(in years)		(in thousands)
Outstanding as of December 31, 2024	1,787,880	$	10.19		9.3	$	—
Granted	—	$	—
Forfeited or expired	(107,056)	$	10.19
Outstanding, vested and expected to vest as of September 30, 2025	1,680,824	$	10.19		8.6	$	—
Exercisable as of September 30, 2025	—	$	—		—	$	—

Valuation of Stock Options Granted under Non-Performance Plans

The weighted-average grant date fair value of stock options granted for the nine months ended September 30, 2025 and 2024 was $3.72 and $10.42 per stock option, respectively.

The fair value of stock options granted for the nine months ended September 30, 2025 and 2024 was estimated using the Black-Scholes option pricing model with the following assumptions:


	Nine Months Ended September 30,
	2025	2024
Expected term (in years)	5.23 - 6.08	5.75 - 6.08
Volatility	98.84% - 104.32%	103.65% - 109.54%
Risk-free interest rate	3.69% - 4.65%	3.47% - 4.48%
Dividend yield	0.00%	0.00%

Expected Term

The expected term represents the weighted-average period the stock options are expected to remain outstanding and is based on the options’ vesting terms and contractual terms, as the Company did not have sufficient historical information to develop reasonable expectations about future exercise patterns and post-vesting employment termination behavior.

Expected Volatility

The expected stock price volatility assumption was determined by examining the historical volatilities for industry peers, as the Company did not have sufficient trading history of its common stock. The Company will continue to use industry peers in determining historical stock price volatility until sufficient historical data of its common stock becomes available.

Risk-Free Interest Rate

The risk-free interest rate assumption is based on the U.S. Treasury instruments whose term was consistent with the expected term of the Company’s stock options.

Dividends

The Company has not paid any cash dividends on common stock since inception and does not anticipate paying any dividends in the foreseeable future. Consequently, an expected dividend yield of zero was used.

ALUMIS INC.

NOTES TO THE CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

(Unaudited)

Valuation of Stock Options Granted under the 2024 POP

Stock options granted under the 2024 POP vest based on service, market and performance conditions (the occurrence of the IPO or a change of control) and are classified as equity financial instruments. At the grant date, the fair value of stock options granted under the 2024 POP was estimated using a Monte Carlo simulation model, which uses a distribution of potential outcomes on a monthly basis over the vesting period prioritizing the most reliable information available. The assumptions utilized in the calculation were based on the achievement of certain stock price thresholds, including the Company’s expected common stock price, expected volatility, risk-free rate and expected term. The Company used the following assumptions to estimate the fair value at the grant date in May 2024: common stock fair value of $12.06, vesting term of 6.0 years, volatility of 122.00%, and risk-free rate of 4.38%. The estimates of fair value are uncertain and changes in any of the estimated inputs could have resulted in significant adjustments to the fair value.

The Company’s estimated fair value of stock options issued under the 2024 POP of $18.0 million is recognized using graded vesting from July 1, 2024, the closing of the IPO, when the performance condition was met, over the longer of (i) the explicit service period of the service condition of 36 months or (ii) the derived service period between 1.4 years to 2.1 years, as determined for each graded vesting tranche.

Early Exercise of Employee Stock Options

Proceeds from the early exercise of stock options are recorded as share repurchase liability, and as shares vest are recognized to additional paid-in capital in the consolidated balance sheets. As of September 30, 2025 and December 31, 2024, share repurchase liability related to unvested shares was $0.2 million and $0.8 million, respectively, and was classified as share repurchase liability in the condensed consolidated balance sheets.

The following table summarizes the activity for the Company’s early exercised shares for the nine months ended September 30, 2025:


		Weighted-
		Average
	Number of	Exercise Price
	Shares	Per Share
Unvested as of December 31, 2024	146,683	$	5.53
Vested	(125,805)	$	4.96
Unvested as of September 30, 2025	20,878	$	8.96

2024 Employee Stock Purchase Plan

In June 2024, the Company’s board of directors adopted, and its stockholders approved, the 2024 ESPP, which became effective on June 28, 2024, upon execution of the underwriting agreement related to the Company’s IPO. The Company initially reserved 650,000 shares of common stock for issuance under the 2024 ESPP. The number of shares of common stock reserved for issuance under the 2024 ESPP will be automatically increased each year for ten calendar years beginning on January 1, 2025 through January 1, 2034, by the lesser of (i) 1% of the total number of shares of our common stock outstanding on the last day of the calendar month before the date of the automatic increase, and (ii) 1,950,000 shares; provided that before the date of any such increase, the board of directors may determine that such increase will be less than the amount in (i) and (ii) above. Pursuant to this evergreen provision, the Company increased the number of shares reserved under the 2024 ESPP by 544,073 on January 1, 2025. The 2024 ESPP allows an eligible employee to purchase shares of common stock at an amount equal to 85% of the lower of the fair market value of the Company’s common stock at the beginning of the offering period or at each applicable purchase date during an offering period as established by the board of directors. The first purchase period commenced on January 24, 2025 and ended on May 20, 2025. During the nine months ended September 30, 2025, 184,633 shares of common stock were purchased under the ESPP.

ALUMIS INC.

NOTES TO THE CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

(Unaudited)

The following table summarizes the Black-Scholes option pricing model used in estimating the fair value of the stock purchase rights under the ESPP during the nine months ended September 30, 2025:


		Nine Months Ended
		September 30, 2025
Expected term (in years)		0.32 - 0.50
Volatility		79.42% - 133.00%
Risk-free interest rate		4.25% - 4.33%
Dividend yield		0.00%

Restricted Stock Units

A summary of unvested RSU activity is presented in the following table:


		Weighted-
		Average
		Grant Date
	Number of	Fair Value
	Shares	Per Share
RSUs assumed in connection with the ACELYRIN Merger	1,470,868	$	13.46
RSUs granted	2,449,945	$	3.95
RSUs released	(1,115,413)	$	13.76
RSUs forfeited	(134,495)	$	5.48
Unvested as of September 30, 2025	2,670,905	$	5.01

Stock-Based Compensation Expense

The following table summarizes the stock-based compensation expense recognized in the Company’s unaudited condensed consolidated statements of operations and comprehensive loss for the three and nine months ended September 30, 2025 and 2024 (in thousands):


	Three Months Ended September 30,				Nine Months Ended September 30,
	2025		2024		2025		2024
Research and development	$	5,773	$	3,720	$	16,717	$	6,805
General and administrative		4,014		3,589		18,700		6,294
Total stock-based compensation expense	$	9,787	$	7,309	$	35,417	$	13,099

ALUMIS INC.

NOTES TO THE CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

(Unaudited)

Stock-based compensation expense included $1.0 million as general and administrative expenses and $1.1 million as research and development expenses for the three months ended September 30, 2025, related to accelerated vesting and exercise term modification for severed employees in connection with the ACELYRIN Merger. Stock-based compensation expense included $8.8 million as general and administrative expenses and $4.1 million as research and development expenses for the nine months ended September 30, 2025, related to accelerated vesting and exercise term modification for severed employees in connection with the ACELYRIN Merger.

The following table summarizes the stock-based compensation expense recognized in the Company’s unaudited condensed consolidated statements of operations and comprehensive loss by award type for the three and nine months ended September 30, 2025 and 2024 (in thousands):


	Three Months Ended September 30,				Nine Months Ended September 30,
	2025		2024		2025		2024
Stock options	$	7,979	$	7,291	$	28,771	$	13,045
RSUs		1,542

Nine Months Ended September 30,

Cash payments included in the measurement of operating lease liabilities

ALUMIS INC. 10-Q