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The phrase "a small but significant difference" is correct and usable in written English.
It can be used to highlight a difference that may seem minor in size or scope but has important implications or effects.
Example: "While the changes to the policy are minimal, they create a small but significant difference in how we approach customer service."
Alternatives: "a minor yet important distinction" or "a slight but meaningful variation".
Exact(60)
Physical fitness showed a small but significant difference in favour of ParkFit, but quality of life did not differ between the ParkFit and control intervention.
I find a small but significant difference in competitiveness between states with political redistricting methods and states with non-political redistricting methods.
Ivanov calls his wife a "dirty Jew" in David Hare's version, but here he says, "you Jew," a small but significant difference.
We're currently facing an acute housing crisis that is particularly affecting young people: we can't build fast enough, so any older households downsizing would be making a small but significant difference to a number of young lives.
The reconstructions with no corrections (FBP and IRNC) display a small but significant difference for both quantification methods (p < 0.001).
There was a small, but significant difference between HC and BD participants for the total EmoBio score (F (1,136) = 4.85, p = 0.029, η 2 = 0.03).
The same trial examined levetiracetam 1000 mg versus topiramate 100 mg and found a small but significant difference favouring topiramate in headache frequency per 28-day period during treatment (MD 1.40; 95% CI 0.14 to 2.66; 28 patients).
On the contrary, a small but significant difference in knowledge was found depending on the level of experience; young radiographers (with less than 3 years of experience) show to have a slight increase in score when compared with older radiographers.
Interestingly, our study also found that there was a small, but significant, difference in the copays at the baseline between saxagliptin and sitagliptin groups (the average difference was $2.18).
It's a small but significant difference.
Shifting your focus to the behavior you want is a small but significant difference.
More suggestions(20)
a minimal but significant difference
a marginal but significant difference
a mild but significant difference
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a small but statistical difference
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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