GET-Evidence reports this variant as occurring in 3 out of 128 randomly selected genomes. Milroy disease is quite rare: GeneTests describes it as unknown prevalence but one of the more common causes of primary lymphedema (hereditary lymphedema). http://www.medscape.com/viewarticle/568789_2 describes incidence of primary lymphedema as occurring in 1.15 out of 100,000.
Taking a generous unknown variant hypothesis — that an unknown causal variant is responsible for causing primary lymphedema in 1 out of 200,000 individuals (half of all cases), and the variant has 50% penetrance — such a variant would be predicted to have an allele frequency of 0.224%. This variant observations (3 out of 128, 2.34%) is highly significantly divergent from such a hypothetical variant (p = 0.0031).