'The effect is quite significant,' says Elad Ziv, professor of medicine at the University of California, San Francisco (UCSF), and co-author of the study.
Women who inherit one copy of the variant - which is the case for roughly one in five Latin American women in the US - have their risk of developing breast cancer reduced by 40 percent, according to the research. Those who inherit two copies are 80 percent less likely to have the disease. Latin women of indigenous American ancestry have a higher chance of inheriting the trait.
Breast cancer is one of the commonest forms of cancer in women. Previous studies show that women of Latin American origin are relatively less likely to have or die from the disease compared to other ethnic groups - and this could be partially due to the effect of the protective variant.
'If we can use these results to better understand how this protects from oestrogen-receptor-negative breast cancer, that would be interesting and important,' Professor Ziv said. 'Because right now we have no good way to prevent that type of breast cancer.'
The precise mechanism through which the SNP protects against breast cancer is not yet known, but early research suggests the variant interferes with the actions of transcription factor protein that regulate expression of the ESR1 receptor.
The study also reports that women with this genetic variation have breast tissue that appears less dense on a mammogram, a factor that has previously been associated with lower risk of breast cancer.
'This is a really important study,' Marc Hurlbert, executive director of the Avon Foundation Breast Cancer Crusade, who was not involved in the study, told The New York Times. 'If we can understand how this is protective, it might help us to develop better treatments for those who do get breast cancer.'
The study was published in Nature Communications.