Yes, "rare sequence variant" as suggested by the people from Department of Speech Communication, University of Georgia and the Oxford English Dictionary, is correct but "rare SNP" isn't and is confusing.
They are not mine, this is how it is referred to in scientific publication. Here are some recent examples for Apoa-I Milano:
Looking at the names of scientists using these terms, makes me feel more comfortable than insulted
The link you've cited contains suggestions and recommendation to prevent confusion, which are very sensible but as you can see from reading the actual publications, the terms mutation, polymorphism and SNP are widely used and understanding the difference between these terms is the key to answer the question raised by urche in #msg-75751678.
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