Discrepancy in BRCA2 SNV counts between main text and appendix

[QIANJINYDX]

Hi authors,

Thank you for releasing the code and data. I have a question regarding the consistency of variant counts.

In the paper, it is stated that:

For BRCA2, SNVs labeled as “P strong”, “P moderate”, and “P supporting” were classified as loss of function variants (N = 1,156), while SNVs labeled as “B strong”, “B moderate”, “B supporting” were classified as functional/intermediate variants (N = 5,681).

However, in the appendix dataset summary, the numbers appear different. For example, according to the table:

• coding SNVs: 470 positive / 2976 negative / 3446 total
• noncoding SNVs: 145 positive / 361 negative / 506 total
• both: 883 positive / 4336 negative / 5219 total

This seems not to align with the (N = 1,156 vs. 5,681) mentioned in the main text.

Could you clarify how the numbers in the appendix were derived, and how they relate to the classification in the main text?

• Are additional filters (e.g., VUS removal, different annotation references like GRCh38 vs. GRCh37, or merging of categories) applied?
• Or is this a matter of reporting different subsets (e.g., coding-only vs. combined)?

Thanks in advance for your clarification!