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Additional notes

  • Tiering is performed using a signed-off version of a panel, with the version most recently approved at the time of interpretation. The gene content of current and previous signed-off versions is available in PanelApp (see Use of virtual gene panels).

  • Tiering of variants on chrX is performed according to an individual’s inferred number of X chromosomes from coverage levels in the genomic data. The number of X chromosomes used in tiering will be the same as used in variant calling (see Genome build, alignment and variant detection), which is displayed in the Interpretation Portal.

  • Tiering supports only haploid and diploid models, thus tiering of variants on chrX may be suboptimal for individuals with minor sex karyotypes with different X chromosome ploidy.

  • A single heterozygous SNV or indel variant identified in a gene with a biallelic mode of inheritance will not be assigned a tier, but can be explored using the decision support system (see Decision Support Systems). Mode of inheritance is not used in CNV tiering, therefore all CNVs that impact genes are assigned a tier (see Copy number variant tiering).

  • The Segregation Filter for de novo variants is considered independently of other segregation filters. The DRAGEN de novo variant detection algorithm considers all variants with a non-Mendelian inheritance pattern, and in rare cases, this can result in variants being inappropriately tiered. For example, a homozygous variant in a proband will be considered as de novo and tiered (with monoallelic mode of pathogenicity and complete penetrance) if it is heterozygous in one parent and homozygous reference in the other parent.

  • The pipeline reports all the classified variants in a structured format and ignores missing values. For example, in a fully penetrant autosomal dominant setting, a variant would be tiered even if it were missing in one of the affected individuals if it passed all of the other necessary criteria.

  • Input genotypes (from the normalised VCF file produced by the Rare Disease Pipeline) can be phased or unphased, but phase information is currently ignored. It is possible to view alignment files (CRAM) through igv.js, and manually assess phase for variants in close proximity.

  • The Tiering algorithm does not prioritise small variants in pseudoautosomal regions, but CNVs in these regions can be prioritised.

  • In a scenario of compound heterozygosity for a large deletion and a small variant, whereby the small variant is detected within the single copy region, tiering of the small variant may indicate prioritisation under the UniparentalIsodisomy mode (with the corresponding CNV likely being in Tier A).

  • Variants on chromosomes other than 1 to 22, the X chromosome and the mitochondrial genome are not currently considered in Tiering, i.e., variants on the Y chromosome or on alternate and decoy contigs are not currently considered for tiering.