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