Permissible and non-permissible combinations of concordant evidence elements (CanVIG-UK consensus)
| Theme | Evidence elements | CanVIG consensus | Notes, references |
| In silico + functional data | PS3 (functional) and PP3 (in silico) | ✔ X | Co-usage permitted for assays of protein function Co-usage not permitted for assays of splicing; in silico evidence incorporated into PS3 for assays of splicing (as per ACGS guidance)4 5 19 21 22 |
| BS3 (functional) and BP4 (in silico) | ✔ X | ||
| PM1 (hot spot) and PP3 (in silico) | ✔ | Co-usage permitted; regional enrichment and in silico prediction largely different evidence types (and evidence from three tools generally incorporated)15 | |
| In silico + variant mechanism | BP4 (in silico) and BP7 (silent variant) | ✔ | Co-usage permitted for synonymous and intronic variants (splicing effect must be excluded) |
| PVS1 (null variant) and PP3 (in silico) | X | Co-usage not permitted; in silico predictors often incorporate variant mechanism. The strongest legitimate evidence item should be selected for inclusion.23 | |
| PM4 (protein length changes) and PP3 (in silico) | X | ||
| BP3 (in-frame del/ins) & BP4 (in silico) | X | ||
| Use of population data | PS4 (case control) and PM2 (absence in controls) | ✔ | Co-usage permitted, provided that a different source of population data is used for each (this can comprise two predefined partitions of gnomAD)5 |
| Phenotypic specificity | PS4 (case control) and PP4 (phenotype specificity) | ✔ | Co-usage permitted, provided that there is a schema predefining distinct data types used for each, thus preventing ‘double counting’ of phenotypic features (eg PP4 is applied for molecular/tumour assay data, indicating specificity at gene level); PS4 is applied at patient level, counting the strength of features in cases and the number of cases/families5 |
| Scaled evidence items | PS2 (de novo confirmed) and PM6 (de novo not confirmed) | X | Co-usage not permitted; either PS2 or PM6 is used, depending on aggregate observations of de novo occurrence (ClinGen Sequence Variant Interpretation Working Group)24 |
| Overlapping/ related evidence | PS1 (same amino acid) and PM5 (same residue) | X | Co-usage not permitted; the strongest legitimate evidence item should be selected for inclusion |
| PM1 (hot spot) and PP2 (low missense rate) | ✔ | Co-usage permitted; there may be both a low rate of benign missense variation at a whole gene/gene region level and a specific mutational hot spot/functional domain | |
| PVS1 (null variant) and PM4 (protein length changes) | X | Co-usage not permitted; this is double counting of two end points of deleterious effect23 | |
| PVS1 (null variant) and PS3 (functional) | ✔ X | Co-usage not permitted for canonical splice variants or non-canonical splice variants (experimental evidence cannot be scored using PS3 if PVS1 is used)23
Co-usage is permitted for assays of protein function where the evidence is not double-counted (eg, truncating variant in last exon of gene scored as PVS1_mod can be combined with PS3 for experimental evidence, demonstrating a significant effect on protein function) | |
| PS1 (same amino acid) and PM1 (hot spot) | ✔* | Co-usage permitted; definition of a hot spot is predicated on multiple well-documented pre-existing pathogenic variants. This may include those at the same amino acid | |
| PM5 (same residue) and PM1 (hot spot) | ✔* | ||
| Alternative explanation for phenotype | BP2 (observed with pathogenic variant) and BP5 (alternative cause) | X | Co-usage not permitted; These evidence elements both pertain to presence of an alternative genetic cause (BP2 in the same gene and BP5 in a different gene) |
*PM1 should therefore be used at supporting level if used in combination with PS1 or PM5.15
ACGS, Association for Clinical Genomic Science; CanVIG-UK, Cancer Variant Interpretation Group UK.