The variant is very rare in population databases, with gnomAD v2.1 total AF 2.04127e-05 (0.00204%) and grpmax FAF 2.326e-05, which are below the generic PM2 rarity threshold of 0.1%.
gnomad_v2 ↗gnomAD v4.1 likewise shows a total AF of 1.44198e-05 (0.00144%) and grpmax FAF 3.005e-05, which remains below the generic PM2 rarity threshold of 0.1% and confirms that the variant is uncommon in the general population.
gnomad_v4 ↗SpliceAI predicts minimal splicing effect, with a maximum delta score of 0.03, which is below the splice-impact threshold of 0.2 and supports BP4.
spliceai ↗ClinVar contains a likely benign classification for this variant with single-submitter review status, which is concordant with a benign leaning but is not used as stand-alone classification evidence.
clinvar ↗Because the available data provide one supporting pathogenic criterion for rarity and one supporting benign criterion for computational evidence against splice disruption, NM_006231.4:c.4006-15C>T is classified as a variant of uncertain significance.
