Table 2 Criteria for assessment of disease association at gene (a) and at variant (b) level
a. Is phenotype applicable to this case (at gene level) | ||
Option | Where to look | When to choose |
Yes | OMIM, HGMD, PubMed | Disease clinical features match patient’s phenotype |
Uncertain/possibly | OMIM, HGMD, PubMed | Disease clinical features partially overlap with patient’s phenotype |
No (clearly unrelated) | OMIM, HGMD, PubMed | No overlapping phenotype, totally different disease |
No/little phenotypic evidence available | OMIM, HGMD, PubMed | Phenotypic evidence was only found in few low-quality papers, or only from association studies, or only somatic mutations were reported |
de novo - No/little phenotypic evidence (chose for variants from de novo filter only) | OMIM, HGMD, PubMed | Same as ‘No/little phenotypic evidence available’, but only for de novo variants |
Reportable secondary finding | OMIM, HGMD, PubMed | Depends on patient’s requirement, mostly for genes associated with actionable diseases. Not limit to genes in ACMG guideline. If the patient does NOT want secondary findings, do NOT choose this option |
b. Interpretive category (at variant level except deleterious VUS) | ||
Option | Where to look | When to choose |
Benign | 1000 Genomes, EVS, ExAC | Allele frequency >1 % for recessive or X-linked patterns. And for X-linked pattern, at least several hemizygous males should be reported in the database. Or allele frequency >0.1 % for dominant or de novo patterns |
Likely benign | UCSC genome browser | Deletion/insertion of 1–2 aa in a repeat region composed of at least 8 aa repeats |
Intronic-likely benign | UCSC genome browser, HGMD, ClinVar | The nomenclature for all transcripts indicates that the change is intronic, but not in canonical splice sites (−1, −2, +1, or +2), except variants reported in HGMD or ClinVar as pathogenic/likely pathogenic |
VUS | Variant which does not fit other categories | |
Deleterious VUS (only chose for genes with no/little phenotype evidence) | UCSC genome browser, ACMG guideline | Variant assumed to disrupt gene function (nonsense, frameshift, canonical splice sites, and so on), but in a gene with no/little phenotype evidence available |
Likely pathogenic | UCSC genome browser, ACMG guideline | Has not been reported before, but is assumed to disrupt gene function (nonsense, frameshift, canonical splice sites, and so on). Or variant which meets ACMG guideline |
Pathogenic | HGMD, ClinVar, OMIM | Well-established disease-causing mutation by previous reports |
Mapping error | UCSC genome browser, IGV, Ingenuity | Variant in segmental duplication or repeat region, and mapping quality/coverage is low. Generally you can see many variant calls in the same region. Also pay attention to complex variants such as large deletions/insertions and indels, please check IGV because nomenclature could be wrong |
CompoundHet error | Ingenuity | Only 1 non-benign variant found in a gene. Only use for variants that pass through the Compound Het filter |