ITGA2B/ITGB3 variants with discordant initial and final classifications
Gene . | cDNA . | Amino acid . | ClinVar assertion . | Initial expert assertion . | Final PD-EP classification . | Criteria applied . |
---|---|---|---|---|---|---|
ClinVar/initial assertion conflicting | ||||||
ITGA2B | 3060+2T>C | VUS | Pathogenic | Likely pathogenic | PVS1_S, PM2_P, PM3_P, PP4_M | |
ITGA2B | 2965G>A | Ala989Thr | VUS | Likely benign | Likely benign | BS1, BP2, BP4 |
ITGA2B | 891+12del | VUS | Benign | Benign | BA1, BP7 | |
ITGB3 | 565C>T | Pro189Ser | Likely pathogenic | VUS | Pathogenic | PS3_M, PM2_P, PM3_S, PP1, PP3, PP4 |
ITGB3 | 1960G>A | Glu654Lys | VUS and likely benign | VUS | Benign | BA1 |
ITGB3 | 1902C>T | Cys634= | Likely benign | VUS | Benign | BA1, BP7 |
Reclassified from VUS | ||||||
ITGA2B | 1234G>A | Gly412Arg | VUS | VUS | Pathogenic | PM2_P, PM3_S, PP3, PP4_S |
ITGA2B | 257T>C | Leu86Pro | N/A | VUS | Pathogenic | PS3_M, PM2, PM3_P, PP3, PP4_S |
ITGA2B | 460_462del | Glu154del | N/A | VUS | Likely pathogenic | PM2_P, PM3_P, PM4, PP4_M |
ITGB3 | 362-1G>A | VUS | VUS | Likely pathogenic | PVS1, PM2_P | |
ITGB3 | 187C>T | Arg63Cys | VUS | VUS | Likely pathogenic | PS3_M, PM2_P, PM3_P, PP3, PP4_M |
ITGB3 | 448A>G | Met150Val | N/A | VUS | Likely pathogenic | PM2_P, PM3, PP3, PP4_M |
ITGB3 | 629G>C | Cys210Ser | N/A | VUS | Likely pathogenic | PS3, PM2_P, PP1, PP3, PP4_M |
ITGB3 | 1458C>G | Cys486Trp | N/A | VUS | Likely pathogenic | PM2_P, PM3, PP3, PP4_S |
ITGB3 | 1594T>C | Cys532Arg | N/A | VUS | Likely pathogenic | PM2_P, PM3, PP3, PP4_S |
ITGB3 | 1595G>A | Cys532Tyr | N/A | VUS | Likely pathogenic | PM2_P, PM3_P, PM5_P, PP3, PP4_M |
Reclassified to VUS | ||||||
ITGA2B | 2852_2853delinsC | Asp951AlafsTer? | N/A | Likely pathogenic | VUS | PVS1_S, PM2_P |
ITGA2B | 889G>C | Ala297Pro | N/A | Likely pathogenic | VUS | PM2_P, PM3_P, PP1, PP4_M |
ITGA2B | 1821G>A | Thr607= | Likely benign | Likely benign | VUS | PP3 |
ITGA2B | 2728-19T>C | N/A | Likely benign | VUS | BP7, PM2_P | |
ITGB3 | 1366A>C | Thr456Pro | Likely pathogenic | Pathogenic | VUS | PM2_P, PM3_P |
ITGB3 | 953 T>C | Leu318Ser | N/A | Likely pathogenic | VUS | PM2_P, PM3_P, PP3, PP4_M |
ITGB3 | 1125+29G>C | N/A | Benign | VUS | BP7, PM2_P |
Gene . | cDNA . | Amino acid . | ClinVar assertion . | Initial expert assertion . | Final PD-EP classification . | Criteria applied . |
---|---|---|---|---|---|---|
ClinVar/initial assertion conflicting | ||||||
ITGA2B | 3060+2T>C | VUS | Pathogenic | Likely pathogenic | PVS1_S, PM2_P, PM3_P, PP4_M | |
ITGA2B | 2965G>A | Ala989Thr | VUS | Likely benign | Likely benign | BS1, BP2, BP4 |
ITGA2B | 891+12del | VUS | Benign | Benign | BA1, BP7 | |
ITGB3 | 565C>T | Pro189Ser | Likely pathogenic | VUS | Pathogenic | PS3_M, PM2_P, PM3_S, PP1, PP3, PP4 |
ITGB3 | 1960G>A | Glu654Lys | VUS and likely benign | VUS | Benign | BA1 |
ITGB3 | 1902C>T | Cys634= | Likely benign | VUS | Benign | BA1, BP7 |
Reclassified from VUS | ||||||
ITGA2B | 1234G>A | Gly412Arg | VUS | VUS | Pathogenic | PM2_P, PM3_S, PP3, PP4_S |
ITGA2B | 257T>C | Leu86Pro | N/A | VUS | Pathogenic | PS3_M, PM2, PM3_P, PP3, PP4_S |
ITGA2B | 460_462del | Glu154del | N/A | VUS | Likely pathogenic | PM2_P, PM3_P, PM4, PP4_M |
ITGB3 | 362-1G>A | VUS | VUS | Likely pathogenic | PVS1, PM2_P | |
ITGB3 | 187C>T | Arg63Cys | VUS | VUS | Likely pathogenic | PS3_M, PM2_P, PM3_P, PP3, PP4_M |
ITGB3 | 448A>G | Met150Val | N/A | VUS | Likely pathogenic | PM2_P, PM3, PP3, PP4_M |
ITGB3 | 629G>C | Cys210Ser | N/A | VUS | Likely pathogenic | PS3, PM2_P, PP1, PP3, PP4_M |
ITGB3 | 1458C>G | Cys486Trp | N/A | VUS | Likely pathogenic | PM2_P, PM3, PP3, PP4_S |
ITGB3 | 1594T>C | Cys532Arg | N/A | VUS | Likely pathogenic | PM2_P, PM3, PP3, PP4_S |
ITGB3 | 1595G>A | Cys532Tyr | N/A | VUS | Likely pathogenic | PM2_P, PM3_P, PM5_P, PP3, PP4_M |
Reclassified to VUS | ||||||
ITGA2B | 2852_2853delinsC | Asp951AlafsTer? | N/A | Likely pathogenic | VUS | PVS1_S, PM2_P |
ITGA2B | 889G>C | Ala297Pro | N/A | Likely pathogenic | VUS | PM2_P, PM3_P, PP1, PP4_M |
ITGA2B | 1821G>A | Thr607= | Likely benign | Likely benign | VUS | PP3 |
ITGA2B | 2728-19T>C | N/A | Likely benign | VUS | BP7, PM2_P | |
ITGB3 | 1366A>C | Thr456Pro | Likely pathogenic | Pathogenic | VUS | PM2_P, PM3_P |
ITGB3 | 953 T>C | Leu318Ser | N/A | Likely pathogenic | VUS | PM2_P, PM3_P, PP3, PP4_M |
ITGB3 | 1125+29G>C | N/A | Benign | VUS | BP7, PM2_P |
Criteria applied with a modified strength are denoted by the criteria followed by _P for supporting, _M for moderate, _S for strong, and _VS for very strong.
cDNA, complementary DNA; N/A, not applicable.