Skip to main content

Table 2 Summary statistics of variant-level data for the eMERGE participants by effect prediction, whether coding with high/moderate impact and lower impact

From: Prospective participant selection and ranking to maximize actionable pharmacogenetic variants and discovery in the eMERGE Network

Impact Other High/Moderate Combined
  (N=1253) (N=532) (N=1785)
Variant Function
3-prime-UTR 26 %(328) 0 %(0) 18 %(328)
5-prime-UTR 6 %(71) 0 %(0) 4 %(71)
intron 30 %(377) 0 %(0) 21 %(377)
intron-near-splice 2 %(19) 0 %(0) 1 %(19)
missense 0 %(3) 95 %(506) 29 %(509)
missense-near-splice 0 %(0) 2 %(10) 1 %(10)
non-coding-exon 0 %(3) 0 %(0) 0 %(3)
splice-acceptor 0 %(0) 1 %(3) 0 %(3)
splice-donor 0 %(0) 0 %(2) 0 %(2)
stop-gained 0 %(0) 2 %(11) 1 %(11)
synonymous 36 %(451) 0 %(0) 25 %(451)
synonymous-near-splice 0 %(1) 0 %(0) 0 %(1)
Prior rsID 67 %(836) 71 %(376) 68 %(1212)
Prior Clinical Association 6 %(72) 18 %(96) 9 %(168)
OMIM 0 %(6) 1 %(3) 1 %(9)
ClinVar 1 %(12) 3 %(17) 2 %(29)
HGMD 2 %(23) 30 %(157) 10 %(180)
Gene List
ABCA1 9 %(114) 8 %(44) 9 %(158)
ABCB1 5 %(63) 6 %(32) 5 %(95)
APOA1 0 %(4) 1 %(6) 1 %(10)
CACNA1S 4 %(55) 9 %(46) 6 %(101)
CYP2C19 2 %(29) 3 %(18) 3 %(47)
CYP2C9 4 %(45) 4 %(19) 4 %(64)
CYP2D6 11 %(139) 10 %(54) 11 %(193)
CYP3A4 4 %(45) 2 %(8) 3 %(53)
CYP3A5 0 %(3) 0 %(0) 0 %(3)
DPYD 4 %(50) 5 %(24) 4 %(74)
HMGCR 5 %(59) 1 %(6) 4 %(65)
KCNH2 7 %(82) 4 %(19) 6 %(101)
LDLR 7 %(84) 3 %(16) 6 %(100)
NAT2 1 %(8) 2 %(13) 1 %(21)
RYR1 11 %(139) 19 %(102) 14 %(241)
RYR2 12 %(149) 8 %(41) 11 %(190)
SCN5A 8 %(98) 8 %(45) 8 %(143)
SLCO1B1 2 %(20) 5 %(25) 3 %(45)
TPMT 3 %(40) 2 %(8) 3 %(48)
VKORC1 2 %(27) 1 %(6) 2 %(33)
Average Depth 295/401/473 347/436/499 308/413/480
GERP −3.44/−0.47/1.61 2.01/3.90/4.82 −2.31/0.49/3.50
CADD 2.12/5.37/8.66 10.34/14.36/18.59 3.10/7.28/11.70
  1. Effect prediction details can be found on the SnpEff web site (Web Resources). In general, single nucleotide variants, structural variation, and copy number variation annotated as having high or moderate impact modify the coding and/or splice regions of a given gene. For the continuous variables average depth, GERP, and CADD, the three numbers represent quartiles of the distributions (25th,50th, and 75th)