Actually, Form N-400, Part 7, Question C refers to all absences since you became a lawful permanent resident. There is no 5-year cutoff for this question.
If you were an LPR at age 6, then you will need to report this absence. You can hire an attorney to remedy the situation and to accompany you to the interview to make sure everything goes smoothly.
You should talk to an attorney to make sure that you are eligible before you apply. Unfortunately, the process can be a lot more complicated than just being here with a valid visa and marrying a citizen. If you hire an attorney instead of a paralegal, you will have more accountability regarding the process. Also, look for an attorney who will attend the interview with you and your spouse.
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Sometimes people are released on the ISAP program, where they have an ankle bracelet or need to check in periodically. If this applies to your friend, he or she should make sure to comply with any restrictions arising from that program. The friend should also make absolutely sure not to miss the court date, or else he/she will be ordered removed (deported) in his/her absence.
If somebody goes to jail and does not have valid legal immigration status, it is very likely that they would be referred to Immigration and Customs Enforcement upon their release and then they could fight to stay in the US before an immigration judge.
In order to get one year extensions of H1B status while the green card process is ongoing, the PERM must be filed prior to the 6th year. If the employer files the PERM in the 6th year, you are not eligible for the 1-year H1B extensions, and you should investigate changing to another status to remain legally in the US.
He is probably eligible for adjustment of status, the process of applying for permanent residence (a green card) within the United States. However, he should talk to an experienced immigration attorney to confirm that he is eligible before you apply and for assistance in the application process, including having the attorney attend the interview with you.
A J1 transfer is done by school officials who coordinate with the State Department. This might be possible if your PhD program would qualify for J1 status.
However, based on the information you provided, you won't be able to do a PhD on a student visa (F1) until you've spent 2 years out of the country or received a waiver of the 2 year foreign residency requirement. We could assist you to try to get a "No Objection" statement from your home country to get the 2 year requirement waived.
On a related note, a federal judge in Massachusetts recently struck down the federal Defense of Marriage Act. This is the law that defines marriage as only between a man and a woman and restricts the immigration benefits available to same-sex couples.
You should contact an experienced immigration attorney to find out what legal options your partner may have.
Based on the information you gave, you should start the processing by petitioning for each of these relatives ASAP. Your sister and brother will not technically be able to "apply for an immigrant visa" until the priority date of their I-130 is current, based on the date you file and the country they are from.
Since your mom is considered an immediate relative, she is exempt from the quota system and will be able to apply for an immigrant visa as soon as the I-130 is approved.
You can see...
In addition to the answers by the other contributors, another possible consequence is that it would probably be extremely difficult or impossible for the US citizen to sponsor a future spouse through marriage or for the alien to ever get a green card through another marriage, even if those marriages are good-faith.