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The phrase "a subtle but significant difference between" is correct and usable in written English.
It can be used when discussing distinctions that may not be immediately obvious but are important in understanding a topic or concept.
Example: "There is a subtle but significant difference between correlation and causation that researchers must understand."
Alternatives: "a nuanced yet important distinction between" or "a fine but crucial difference between".
Exact(1)
Our data reveal a subtle but significant difference between male and female Tau mice: The firing stability of CA1 neurons on familiar trajectories in female is greater than that in male mice.
Similar(59)
It is important to note a subtle, but significant, difference in the nature of information provided between the two datasets.
Intragroup cluster and discriminant analysis revealed that CANTAB, as compared to language tests, was able to detect subtle but significant differences between the subjects.
At the basal uninduced level, we found subtle but significant differences in gene expression between Wt and Tyk2-/ macrophages.
Along with the changes in body composition, we found subtle but significant differences in IGF-I and TSH Z-score between the exposed and unexposed children.
There is a subtle but unmistakable class difference between them.
For there is a subtle and important difference between the truth and what is true.
It's come to my attention that not everyone understands the subtle yet significant differences between GSM and CDMA.
The mistake amplified a significant difference between Irwin and Fleisher.
That was a significant difference between NEU! and Harmonia.
However, the difference is only subtle with a two sample t-test revealing no significant difference between the values corresponding to each search method.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com