Update normal allele range #309
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dnil
reviewed
Dec 9, 2025
| "DisplayRU": "GCC", | ||
| "Disease": "FRAXE", | ||
| "NormalMax": 39, | ||
| "NormalMax": 69, |
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And this appears to have transferred from the previous PR. Kind bot, but not as intended.
Suggested change
| "NormalMax": 69, | |
| "NormalMax": 39, |
| "DisplayRU": "GCC", | ||
| "Disease": "FRAXE", | ||
| "NormalMax": 39, | ||
| "NormalMax": 69, |
There was a problem hiding this comment.
Suggested change
| "NormalMax": 69, | |
| "NormalMax": 39, |
| "benign_min": 4, | ||
| "benign_max": 39, | ||
| "intermediate_min": 40, | ||
| "benign_max": 69, |
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Suggested change
| "benign_max": 69, | |
| "benign_max": 39, |
| "benign_max": 39, | ||
| "intermediate_min": 40, | ||
| "benign_max": 69, | ||
| "intermediate_min": 70, |
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Suggested change
| "intermediate_min": 70, | |
| "intermediate_min": 40, |
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Name
Daniel Nilsson
Username
@dnil
Email
[email protected]
Description
We are seeing many normal individuals with far larger sizes than expected. The issue appears to be that the current locus definition includes flanking sequence (corresponding to the hg38 masked region) that has GCC trinucleotides. These are then counted towards pathogenic. If there are no other concerns here, adjusting the limits to the primary repeat should solve the issue. For reference, see e.g. Silva et al 2021, specifically figure S1, where some of the spurious surrounding GCCs are evident. Note that the common allele (15 copies) corresponds to the reference genome allele for hg19 and hg38, and that the size of the pathologic repeat should be 45 nt, whereas T2T CHM13 ts1 has 16 copies.