A Yates-corrected Chi-square test revealed the association between AFF3 variants and cutaneous, articular, and vascular impairment, ILD, and esophagitis (χ2 = 19.1–44.8, p < 0.0001); a weak association was found with Sjögren’s syndrome (χ2 = 7.4, p < 0.001). Here, AFF3 is linked to interstitial lung disease.