Thanks for all these additional information.
I understand your concern.
Well as you describe,with protected sex,chances of pregnancy are very less likely if there is no tear in condom.
You are most likely safe and there is no need to worry.
You should do urine pregnancy test after a week from your missed period with a morning urine sample for a precautionary measure.
Other possible cause may include PCOS,hormonal imbalance.
Let me know if you have any further query so we can discuss it thoroughly in every aspect.
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