Some unique Luzon Agta forms have some tempting parallels with Proto-Trans-New Guinea. However, it is likely that these are due to chance resemblance. Pre-Luzon Agta should be considered to be an independent phylum, or phyla with no connections elsewhere.
Comparisons below are from the ABVD.
hand
Mindoro areal word *dalúkap
Batangan daluwáp 3, 44 A:M:P:G:S:Buhid-Taubuid
Buhid daluáp 3, 44 A:M:P:G:S:Buhid-Taubuid
Hanunoo dalúkap 3, 44 A:M:P:G:S:Hanunoo
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Alangan dalukap 3, 44 A:M:P:North Mangyan
Tadyawan dalúkap 3, 44 A:M:P:North Mangyan
Tadyawan dukap 3, 67 A:M:P:North Mangyan
fear
Inati *gɨláng
Inati (Hamtic) gɨláng M:G:C:B:C:P
Inati (Jordan, Guimaras) gɨláng M:G:C:B:C:P
snake
Southern Luzon Agta *bebek
Ayta Abellen bikat M:P:C:S
Proto-Manide-Alabat *béʔek M:P:G:U
Manide púo M:P:G:U
Umiray Dumaget bebek M:P:G:U
fire
Agta *dukut
15. fire *dukut North Agta, Arta
Arta du:t M:P:N:A
149. fire *adiŋ South Agta
Inati *himpon
Inati (Hamtic) himpon M:G:C:B:C:P
Inati (Jordan, Guimaras) hímpon M:G:C:B:C:P
Inati (Nagpana) himpon M:P:G:C:B:C:P
Sogodnin (Boracay) yimpon M:P:G:C:B:C:P
Sogodnin (Iloilo) himpon M:P:G:C:B:C:P
Mamanwa gabok M:P:G:C:M
Northern Mindoro *bayaʔ
Iraya bayâ 43 M:P:N
Alangan baya 43 M:P:N
Tadyawan bayâ 43 M:P:N
Tadyawan bä 43 M:P:N
Dupaningan Agta gangatan M:P:N:N:N:N
feather
16. hair, feather *pulug North Agta, Arta
Ayta Abellen polokpok M:P:C:S
Umiray Dumaget putput M:P:G:U
Proto-Manide-Alabat *gitgít M:P:G:U
Manide gitgit M:P:G:U
leaf
154. leaf *hayin Sinauna
Sinauna háyin M:P:C:S
26. leaf *agid Alta, Central Agta
Umiray Dumaget agid M:P:G:U
Buhid labong M:P:G:S:B
Alangan labong M:P:N
Tadyawan giráng M:P:N
Tadyawan gilang M:P:N
Kapampangan bulúŋ 18 M:P:C:P
Kapampangan bulung 18 M:P:C:P
Sambal, Botolan bo'long 18 M:P:C:S
Ayta Mag-antsi bulong 18 M:P:C:S
male
27. man, male *patud Alta, Central Agta
Inati (Hamtic) alíwas M:G:C:B:C:P
Inati (Nagpana) aliwas M:P:G:C:B:C:P
Inati (Jordan, Guimaras) ámos M:G:C:B:C:P
Inati (Nagpana) amos 106 M:P:G:C:B:C:P
Sogodnin (Iloilo) amus 106 M:P:G:C:B:C:P
Mamanwa ʔamaʔama M:P:G:C:M
Batangan baguama young man M:P:G:S:B
sleep
38. sleep *puləd North Alta, South Alta
143. sleep *pida Central Agta
Manide píges M:P:G:U
Umiray Dumaget pede M:P:G:U
Ayta Mag-indi bɨlɨw M:P:C:S
Bolinao ɨlɨk M:P:C:S
salt
67. salt *b[ia]gəl North Agta
Batak, Palawan budbud 24 M:P:G:P
water
147. water, river *urat Central Agta
Umiray Dumaget orat M:P:G:U
Arta wagət 2 M:P:N:A
Tadyawan lubóng M:P:N
rat
2. rat *kuyəŋ North Agta, Alta, Central Agta
Umiray Dumaget kuyoŋ M:P:G:U
Dumagat, Casiguran ku'yɨng M:P:N:N:N:N
Dupaningan Agta kuyang M:P:N:N:N:N
Arta bukət M:P:N:A
Atta, Pamplona ulak M:P:N:N:C:I
Agta bʌlʌkʌd 41 M:P:N:N:C:I:G
Dupaningan Agta bilakad M:P:N:N:N:N
Umiray Dumaget kuragbeŋ M:P:G:U
bone
128. bone *kaks(-an) Central Agta
Umiray Dumaget kaksan M:P:G:U
Mamanwa bɨkɨg 16 M:P:G:C:M
Proto-Manide-Alabat *beyán 47 M:P:G:U
Manide beyón 47 M:P:G:U
70. bone *sagnit Arta
wind
157. wind *rugus Sinauna
Sinauna rú'gus M:P:C:S
Batak, Palawan dɨrɨs 36 M:P:G:P
Buhid durós 82 M:P:G:S:B
Umiray Dumaget palos 48 M:P:G:U
Dumagat, Casiguran pa'hɨs 48 M:P:N:N:N:N
Dupaningan Agta paras 48 M:P:N:N:N:N
(Old Central Luzon areal form?)
Proto-Manide-Alabat *hiʔnéw M:P:G:U
Manide hi-néw M:P:G:U
Arta bəgbəg 27, 84 M:P:N:A
Atta, Pamplona padda:k 27, 85 M:P:N:N:C:I
Agta pʌddad 27, 85 M:P:N:N:C:I:G
wing
53. wing *kəpig North Agta
Dupaningan Agta kappeg M:P:N:N:N:N
ear
Zambalic Ayta *tɨk
Ayta Mag-antsi têkk 45 M:P:C:S
Ayta Ambala tɨk 45 M:P:C:S
Ayta Mag-anchi tɨːk 45 M:P:C:S
Ayta Mag-indi tɨk 45 M:P:C:S
Proto-Manide-Alabat *sewéŋ M:P:G:U
Manide sewéng M:P:G:U
73. ear *ibəŋ Arta
Arta ibəŋ M:P:N:A
Agta bʌngbʌng M:P:N:N:C:I:G
rain
139. rain *tapuk Central Agta
Umiray Dumaget tapok M:P:G:U
Batak, Palawan lɨbɨg 21 M:P:G:P
Bolinao rapɨg M:P:C:S
(Old Central Luzon area form?)
Proto-Manide-Alabat *gemés M:P:G:U
Manide gemés M:P:G:U
Arta pu:nəd M:P:N:A
Inati (Hamtic) dáʔit M:G:C:B:C:P
Inati (Jordan, Guimaras) dáʔit M:G:C:B:C:P
Inati (Nagpana) daʔit M:P:G:C:B:C:P
Ayta Ambala abagat M:P:C:S
mosquito
150. mosquito *kubuŋ South Agta [Manide]
Atta, Pamplona agupu:ʔ 29 M:P:N:N:C:I
Mindanao areal word
Iraya tagnók M:P:N
Mamanwa tagnɨk 27 M:P:G:C:M
Proto-Manide-Alabat *peléŋot M:P:G:U
Manide peléngot M:P:G:U
124. true *kuduR South Alta
Atta, Pamplona kurrug 83 M:P:N:N:C:I
tail
121. tail *lambuŋ South Alta
Inati (Jordan, Guimaras) tubáng M:G:C:B:C:P
Inati (Nagpana) toban M:P:G:C:B:C:P
Sogodnin (Iloilo) toben M:P:G:C:B:C:P
heavy
39. heavy *dəgi North Agta
Dumagat, Casiguran mɛdɨ'giʔ 1, 62 M:P:N:N:N:N
Dupaningan Agta madaggi 1, 62 M:P:N:N:N:N
Arta dəttun M:P:N:A
thick
40. thick *bagəl North Agta
Arta bagəl 62 M:P:N:A
Dumagat, Casiguran ba'gɨl L M:P:N:N:N:N
Dupaningan Agta mabigal 62 M:P:N:N:N:N