Table 2.
Characteristics of loci incorporated in the BCAC 313 or BRIDGES 306 breast cancer PRSs that were either not included in the gnomAD v3.1.2 database or reported with extremely deviating allele frequency compared to CanRisk.
| CanRisk log OR |
gnomAD v3.1.2 | |||||
|---|---|---|---|---|---|---|
| rs ID | Locus (hg19) | BCAC | BRIDGDES | AF | AF | Comment |
| rs56168262 | 1-51467096-CT-C | 0.0374 | 0.0374 | 0.4856 | 0.3969 | LCR |
| rs56097627 | 1-110198129-CAAA-C | 0.0458 | 0.0458 | 0.7779 | 0.0681 | LCR |
| rs143384623 | 1-145604302-C-CT | −0.0399 | −0.0399 | 0.3490 | 0.3764 | LCR |
| rs78425380 | 2-10138983-T-C | 0.0603 | 0.1168 | 0.0085 | LCR, LQS | |
| rs553796823 | 2-39699510-C-CT | −0.0402 | −0.0402 | 0.4647 | 0.5134 | LCR |
| rs572022984 | 2-217955896-GA-G | −0.2016 | −0.2016 | 0.0364 | Allele count zero | |
| rs774021038 | 4-84370124-TA-T | −0.0464 | −0.0464 | 0.5353 | 0.5030 | LCR |
| rs147404208 | 4-92594859-TTCTTTC-T | −0.0407 | 0.4386 | 0.4911 | LCR | |
| rs62331150 | 4-106069013-G-T | 0.0471 | 0.0471 | 0.2286 | 0.4214 | LQS |
| rs113778879 | 5-58241712-C-T | −0.0434 | 0.5762 | Not listed in gnomAD | ||
| rs543824204 | 6-20537845-CA-C | −0.0391 | −0.0391 | 0.4741 | 0.3405 | LCR |
| rs574103382 | 6-82263549-AAT-A | 0.0477 | 0.4240 | 0.3242 | LCR | |
| rs73754909 | 6-87803819-T-C | 0.0383 | 0.0383 | 0.2809 | Not listed in gnomAD | |
| rs60954078 | 6-151955914-A-G | 0.1449 | 0.1449 | 0.0726 | 0.1519 | LCR |
| rs57589542 | 6-152022664-CAAAAAAA-C | 0.0137 | 0.0137 | 0.6130 | 0.5048 | LCR |
| rs10644978 | 7-91459189-A-ATT | 0.0452 | 0.0452 | 0.3332 | 0.3675 | LCR |
| rs111963714 | 7-99948655-T-G | 0.0420 | 0.0420 | 0.2083 | 0.1425 | |
| rs5887960 | 7-139943702-CT-C | 0.0582 | 0.0582 | 0.5378 | 0.4091 | LCR |
| rs3988353 | 8-17787610-CT-C | −0.0377 | −0.0377 | 0.6217 | 0.4462 | LCR, VQSR |
| rs3057314 | 9-21964882-CAAAA-C | 0.0550 | 0.0550 | 0.3210 | 0.2794 | LCR |
| rs2384736 | 10-38523626-C-A | 0.0404 | 0.0404 | 0.3740 | 0.0003 | LCR, LQS |
| rs111833376 | 10-71335574-C-T | −0.0404 | 0.3122 | 0.3122 | 0.0699 | LCR |
| rs140936696 | 10-95292187-CAA-C | −0.0512 | −0.0512 | 0.8177 | 0.7074 | LCR |
| rs10862899 | 12-85004551-C-T | 0.0348 | 0.0348 | 0.4999 | 0.5259 | |
| rs57920543 | 16-4008542-CAAAAA-C | −0.0329 | −0.0329 | 0.8194 | 0.7400 | LCR |
| rs79461387 | 17-29168077-G-T | −0.0568 | −0.0568 | 0.2573 | Not listed in gnomAD | |
| rs2668667 | 17-44283858-G-A | −0.0540 | −0.0540 | 0.1919 | 0.1586 | |
| rs112855987 | 22-45319953-G-A | −0.0134 | 0.4158 | 0.5272 | LCR | |
Log odds ratios (ORs) are identical for BCAC 313 and BRIDGES 306, but missing values indicate loci not included in the corresponding PRS. Entries in the Comment column refer to technical artifacts reported in gnomAD.
LCR low-complexity region, LQS low-quality site (in <50% of samples covered), VQSR failed allele-specific GATK Variant Quality Score Recalibration (VQSR) filter.