I did a quick read of the
Nature Genetics letter and, as far as I can tell, it makes no claims as to the worldwide frequency of the allele (actually a micro-deletion). Accurately measuring allele frequencies for the world's population is not something that most studies are adequately designed for, so it's not surprising that they don't provide an estimate.
Here's what they have to say about the deletion's frequency outside of India.
The presence of this deletion in many Indian populations with varied geographical and ancestral backgrounds raises the question of how geographically widespread it is outside India. We therefore also analyzed 63 world population samples, comprising 2,085 indigenous individuals from 26 countries including all five continents. The 25-bp deletion was observed in Pakistan, Sri Lanka, Indonesia and Malaysia, (all heterozygotes) but was absent from other samples. Thus, the deletion is a common variant in individuals from South Asia, present in Southeast Asia, but undetectable elsewhere (Fig. 3 and Supplementary Table 5 online).
The supplementary materials give the sample sizes for each of the ethnic groups that were sampled and the number of deletion carriers. Most of the individual samples are small, but in the aggregate they do strongly suggest that the deletion is practically non-existent outside of South Asia and a few neighboring areas.
This does raise the question of how the media got this 1% prevalence estimate, unless I completely missed it in the article. In general, media outlets don't report the contents of peer-reviewed articles, they report the contents of press releases that accompany (or precede) the articles.