Table 3.
Variants in risk-associated genes
| Gene | Coding change | dbSNP/ClinVar | Classification | ExAC | 1000G | CADD | Local ancestry |
|---|---|---|---|---|---|---|---|
| ABCA7 | c.2T>C | rs1347920426 | PTV (nonsense) | . | . | 24.9 | Native American |
| c.236A>C (p.Asn79Thr) | rs377401443 | SD | 4.16E-05 | . | 24.5 | African | |
| c.1180_1190del (p.Leu396fs) | rs567222111 | PTV (frameshift) | 0.0005 | 0.0022 | . | African | |
| c.1531G>T (p.Glu511*) | rs374932832 | PTV (nonsense) | 7.60E-05 | . | 39 | African | |
| c.1776G>T (p.Trp592Cys) | SCV001751545 | SD | . | . | 26 | African | |
| c.2124_2130del (p.Glu709fs)+ | rs547447016 | PTV (frameshift) | 0.0024 | 0.0006 | . | European | |
| c.2194C>T (p.Gln732*) | rs1030634619 | PTV (nonsense) | . | . | 36 | European | |
| c.2552+11_2552+58del | rs1178315251 | PTV (splice) | . | . | . | African | |
| c.2611G>C (p.Asp871His) | rs139251928 | SD | 0.0004 | 0.0014 | 24.8 | African | |
| c.3781delC (p.Pro1261fs) | SCV001751546 | PTV (frameshift) | . | Native American | |||
| c.4208delT (p.Leu1403fs) | rs538591288 | PTV (frameshift) | 0.0011 | . | . | European | |
| c.4465C>T (p.Arg1489*) | rs753664323 | PTV (nonsense) | 6.66E-05 | . | 39 | European | |
| c.4886C>T (p.Ser1629Leu)+ | rs184590335 | SD | 0.0012 | 0.0006 | 35 | Native American | |
| c.4895C>T (p.Pro1632Leu) | rs143083561 | SD | 0.0002 | 0.0006 | 34 | African | |
| c.5302delC (p.Leu1768fs) | rs1348650979 | PTV (frameshift) | . | . | . | Native American | |
| c.5463+2T>C | rs374611445 | PTV (splice) | 2.81E-05 | . | 23.7 | European | |
| c.5794C>T (p.Arg1932C) | rs114787084 | SD | 0.0002 | 0.0006 | 34 | African | |
| SORL1 | c.994C>T (p.Arg332Trp) | rs772110877 | SD | 5.77E-05 | . | 35 | European |
| c.1432G>C (p.Ala478Pro) | SCV001751547 | SD | . | . | 28.2 | European | |
| c.1496C>T (p.Ser499Leu) | rs764032259 | SD | 8.24E-06 | . | 35 | European | |
| c.2200G>A (p.Asp734Asn) | rs148430425 | SD | 0.0011 | . | 34 | European | |
| c.2230C>T (p.Arg744*) | rs1050845490 | PTV (nonsense) | . | . | 39 | European | |
| c.2710C>T (p.Arg904Trp) | rs148966249 | SD | 4.12E-05 | 2.00E-04 | 33 | Native American | |
| c.3679G>T (p.Gly1227Cys) | rs1765488318 | SD | . | . | 34 | European | |
| c.4520C>T (p.Pro1507Leu) | rs1308522330 | SD | . | . | 26.2 | Undetermined | |
| c.6550G>A (p.Ala2184Thr) | rs369618646 | SD | 4.16E-05 | . | 34 | African | |
| TREM2 | c.140G>A (p.Arg47His)+ | rs75932628 | SD | 0.0021 | 0.002 | 33 | European |
| c.469C>T (p.His157Tyr)+ | rs2234255 | SD | 0.0036 | 0.0028 | 23.1 | Native American | |
|
c.287C>A (p.Thr96Lys) c.572G>A(p.Trp191*) c.632T>C (p.Leu211Pro) |
rs2234253 rs2234258 rs2234256 |
PTV (nonsense) | African | ||||
| c.594G>A (p.Trp198*) | rs1765488318 | PTV (nonsense) | . | . | 39 | Undetermined | |
| ADAM10 | c.510G>C (p.Gln170His)+ | rs61751103 | SD | 0.0012 | 0.0012 | 19.17 | European |
PTV protein truncating variant, SD strictly damaging, ExAC ExAC database minor allelic frequency. CADD corresponds to the Phred score. Variants denoted with a + were identified in homozygous states. GenBank transcripts for each gene can be found in Additional file 4: Table S3