DE NOVO: Het in proband, high coverage homo ref in both parents
POSSIBLY DE NOVO: Het in proband, homozygous ref in both parents where at least one is low coverage
NEWLY HOMOZYGOUS: High coverage homozygous in proband, het in both parents (any coverage)
UNLIKELY NEWLY HOMOZYGOUS: Homozygous in proband and high coverage homozygous ref in one or both parents UNLESS one parent is high coverage homozygous variant
POSSIBLY NEWLY HOMOZYGOUS: Homozygous in proband and Low coverage anything in both parents unless het in both; High coverage het in one parent and low coverage anything in the other; High coverage het in both parents ONLY IF low coverage homo in proband
COMPOUND DELETION: One allele is a SNV and the 2nd allele is a deletion
NO FLAG: Proband homo variant, one parent high coverage homo variant; Proband het unless both parents are homo non-carriers
Denovo Flag (sex chr):
NEWLY HEMIZYGOUS: Proband hemizygous variant, mother high coverage het
UNLIKELY DE NOVO OR NEWLY HEMIZYGOUS: Proband heterozygous, mother homozygous reference
NEWLY HEMIZYGOUS OR POSSIBLE DE NOVO: Proband hemizygous variant, mother low coverage homo ref
POSSIBLY NEWLY HEMIZYGOUS: Proband hemizygous variant, mother low coverage het
NO FLAG: Male het, mother homo variant
Inherited From: Father or Mother or NA
Denovo HZ[E]: hot zone de novo mutation found in an essential (mouse lethality based on the MGI) gene
ClinGen/Var [LoF]: LoF variant found in a ClinGen defined dosage sensitive gene, or a gene where at least one ClinVar "Pathogenic" loss-of-function allele has been reported
LoF depleted/pLI: A protein-truncating predicted de novo allele found in a gene reported to be loss-of-function depleted (FDR<0.01, Petrovski et al.), or defined as LoF intolerant based on the ExAC paper (p>0.9). Restricted to de novo mutations. For recessive genotypes (HEM, HOM, CHET), pLI/pREC>0.9.
Compound Var: comphet variants' identifier with #1 refers to 1st var and #2 for 2nd var.
Var Ctrl Freq #1 & #2 (co-occurance): co-occurance frequency for comphet within default 10k control cohorts.
Tier Flag (Compound Var): Tier 1 or Tier 2 for comphet.
Tier Flag (Single Var): Tier 1 or Tier 2 for singleton variants.