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That is not a trivial problem, even when you find a variant that could be causing the phenotype, a lot of evidence and expertise is required to validate that. There is not a single program or platform that can do that for you. But if you want to explore your data, there are VEP and Exomiser tools, but be aware those are not diagnostic tools.
NOTE:
The number of mentions on this list indicates mentions on common posts plus user suggested alternatives.
Hence, a higher number means a more popular project.
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