Simple Walkthrough¶
Overview¶
The purpose of this walkthrough will be to illustrate a simple, but complete example of using gNALI to find high-confidence loss-of-function variants of genes.
Input Data¶
The input file should contain a list of genes as HGNC symbols, separated by a newline character. Genes in non-standard formats will not be analyzed.
The example input file located in the following location:
inputs/genes.txt
The example input file contains the following contents and can be found here:
> cat inputs/genes.txt
CCR5
ALCAM
Running gNALI¶
gNALI only requires an input file, and has other optional parameters. We will use an input file with the path inputs/genes.txt, filter for high-confidence loss-of-function variants, and write our results to a directory called output-simple.
Since we have not selected a database to use, gNALI will default to gnomADv2.1.1.
Here is what such a command would look like:
gnali
--input inputs/genes.txt
--output output-simple/
Output¶
By default, gNALI will have two output files in output-simple/: a basic output file, and a detailed output file. When using the -v/--vcf flag, a third additional output file will be generated. An example of such output can be found in the advanced walkthrough. More information on outputs can be found here.
Output files for this example can be found here.
Basic Output¶
The basic output file contains a subset of the input genes, the ones that have high-confidence loss-of-function variants that pass filtering. It also contains a list of genes that could not be found in the specified database, if any.
The file shown below can also be found here.
output-simple/Nonessential_Host_Genes_\(Basic\).txt:
| HGNC_Symbol | Status |
|---|---|
| CCR5 | HC LoF found |
| ALCAM | HC LoF found |
Detailed Output¶
The detailed output file contains the high-confidence loss-of-function variants that pass filtering with some annotations extracted.
The file shown below can also be found here.
output-simple/Nonessential_Host_Genes_\(Detailed\).txt:
| Chromosome | Position_Start | RSID | Reference_Allele | Alternate_Allele | Score | Quality | LoF_Variant | LoF_Annotation | HGNC_Symbol | Ensembl_Code | HGVSc |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 3 | 46414403 | rs748244565 | CAA | C | 2676.90 | PASS | - | frameshift_variant | CCR5 | ENSG00000160791 | ENST00000292303.4:c.11_12delAA |
| 3 | 46414403 | rs748244565 | CAA | C | 2676.90 | PASS | - | frameshift_variant | CCR5 | ENSG00000160791 | ENST00000343801.4:c.11_12delAA |
| 3 | 46414403 | rs748244565 | CAA | C | 2676.90 | PASS | - | frameshift_variant | CCR5 | ENSG00000160791 | ENST00000445772.1:c.11_12delAA |
| 3 | 46414434 | rs758662716 | AT | A | 4280.25 | PASS | - | frameshift_variant | CCR5 | ENSG00000160791 | ENST00000292303.4:c.43delT |
| 3 | 46414434 | rs758662716 | AT | A | 4280.25 | PASS | - | frameshift_variant | CCR5 | ENSG00000160791 | ENST00000343801.4:c.43delT |
| 3 | 46414434 | rs758662716 | AT | A | 4280.25 | PASS | - | frameshift_variant | CCR5 | ENSG00000160791 | ENST00000445772.1:c.43delT |
| 3 | 46414436 | rs200209014 | TA | T | 58824.12 | PASS | - | frameshift_variant | CCR5 | ENSG00000160791 | ENST00000292303.4:c.44delA |
| 3 | 46414436 | rs200209014 | TA | T | 58824.12 | PASS | - | frameshift_variant | CCR5 | ENSG00000160791 | ENST00000343801.4:c.44delA |
| 3 | 46414436 | rs200209014 | TA | T | 58824.12 | PASS | - | frameshift_variant | CCR5 | ENSG00000160791 | ENST00000445772.1:c.44delA |
| 3 | 46414443 | rs369206494 | C | A | 73505.83 | PASS | A | stop_gained | CCR5 | ENSG00000160791 | ENST00000292303.4:c.50C>A |
| 3 | 46414443 | rs369206494 | C | A | 73505.83 | PASS | A | stop_gained | CCR5 | ENSG00000160791 | ENST00000343801.4:c.50C>A |
| 3 | 46414443 | rs369206494 | C | A | 73505.83 | PASS | A | stop_gained | CCR5 | ENSG00000160791 | ENST00000445772.1:c.50C>A |
| 3 | 46414453 | rs760428955 | C | A | 2656.37 | PASS | A | stop_gained | CCR5 | ENSG00000160791 | ENST00000292303.4:c.60C>A |
| 3 | 46414453 | rs760428955 | C | A | 2656.37 | PASS | A | stop_gained | CCR5 | ENSG00000160791 | ENST00000343801.4:c.60C>A |
| 3 | 46414453 | rs760428955 | C | A | 2656.37 | PASS | A | stop_gained | CCR5 | ENSG00000160791 | ENST00000445772.1:c.60C>A |
| 3 | 46414454 | rs780235820 | C | CA | 3750.42 | PASS | A | frameshift_variant | CCR5 | ENSG00000160791 | ENST00000292303.4:c.67dupA |
| 3 | 46414454 | rs780235820 | C | CA | 3750.42 | PASS | A | frameshift_variant | CCR5 | ENSG00000160791 | ENST00000343801.4:c.67dupA |
| 3 | 46414454 | rs780235820 | C | CA | 3750.42 | PASS | A | frameshift_variant | CCR5 | ENSG00000160791 | ENST00000445772.1:c.67dupA |
| 3 | 46414457 | rs768398484 | A | T | 2699.39 | PASS | T | stop_gained | CCR5 | ENSG00000160791 | ENST00000292303.4:c.64A>T |
| 3 | 46414457 | rs768398484 | A | T | 2699.39 | PASS | T | stop_gained | CCR5 | ENSG00000160791 | ENST00000343801.4:c.64A>T |
| 3 | 46414457 | rs768398484 | A | T | 2699.39 | PASS | T | stop_gained | CCR5 | ENSG00000160791 | ENST00000445772.1:c.64A>T |
| 3 | 46414541 | rs747388089 | CT | C | 6002.15 | PASS | - | frameshift_variant | CCR5 | ENSG00000160791 | ENST00000292303.4:c.149delT |
| 3 | 46414541 | rs747388089 | CT | C | 6002.15 | PASS | - | frameshift_variant | CCR5 | ENSG00000160791 | ENST00000343801.4:c.149delT |
| 3 | 46414541 | rs747388089 | CT | C | 6002.15 | PASS | - | frameshift_variant | CCR5 | ENSG00000160791 | ENST00000445772.1:c.149delT |
| 3 | 46414604 | rs769057798 | AACCTGGC | A | 2763.36 | PASS | - | frameshift_variant | CCR5 | ENSG00000160791 | ENST00000292303.4:c.212_218delACCTGGC |
| 3 | 46414604 | rs769057798 | AACCTGGC | A | 2763.36 | PASS | - | frameshift_variant | CCR5 | ENSG00000160791 | ENST00000343801.4:c.212_218delACCTGGC |
| 3 | 46414604 | rs769057798 | AACCTGGC | A | 2763.36 | PASS | - | frameshift_variant | CCR5 | ENSG00000160791 | ENST00000445772.1:c.212_218delACCTGGC |
| 3 | 46414651 | rs777330502 | G | A | 25606.70 | PASS | A | stop_gained | CCR5 | ENSG00000160791 | ENST00000292303.4:c.258G>A |
| 3 | 46414651 | rs777330502 | G | A | 25606.70 | PASS | A | stop_gained | CCR5 | ENSG00000160791 | ENST00000343801.4:c.258G>A |
| 3 | 46414651 | rs777330502 | G | A | 25606.70 | PASS | A | stop_gained | CCR5 | ENSG00000160791 | ENST00000445772.1:c.258G>A |
| 3 | 46414696 | rs1800560 | T | A | 540878.23 | PASS | A | stop_gained | CCR5 | ENSG00000160791 | ENST00000292303.4:c.303T>A |
| 3 | 46414696 | rs1800560 | T | A | 540878.23 | PASS | A | stop_gained | CCR5 | ENSG00000160791 | ENST00000343801.4:c.303T>A |
| 3 | 46414696 | rs1800560 | T | A | 540878.23 | PASS | A | stop_gained | CCR5 | ENSG00000160791 | ENST00000445772.1:c.303T>A |
| 3 | 46414697 | rs1294651548 | C | T | 5088.14 | PASS | T | stop_gained | CCR5 | ENSG00000160791 | ENST00000292303.4:c.304C>T |
| 3 | 46414697 | rs1294651548 | C | T | 5088.14 | PASS | T | stop_gained | CCR5 | ENSG00000160791 | ENST00000343801.4:c.304C>T |
| 3 | 46414697 | rs1294651548 | C | T | 5088.14 | PASS | T | stop_gained | CCR5 | ENSG00000160791 | ENST00000445772.1:c.304C>T |
| 3 | 46414702 | rs56068070 | CTT | C | 19747.17 | PASS | - | frameshift_variant | CCR5 | ENSG00000160791 | ENST00000292303.4:c.310_311delTT |
| 3 | 46414702 | rs56068070 | CTT | C | 19747.17 | PASS | - | frameshift_variant | CCR5 | ENSG00000160791 | ENST00000343801.4:c.310_311delTT |
| 3 | 46414702 | rs56068070 | CTT | C | 19747.17 | PASS | - | frameshift_variant | CCR5 | ENSG00000160791 | ENST00000445772.1:c.310_311delTT |
| 3 | 46414714 | rs1249868905 | C | CTA | 1526.36 | PASS | TA | frameshift_variant | CCR5 | ENSG00000160791 | ENST00000292303.4:c.323_324dupAT |
| 3 | 46414714 | rs1249868905 | C | CTA | 1526.36 | PASS | TA | frameshift_variant | CCR5 | ENSG00000160791 | ENST00000343801.4:c.323_324dupAT |
| 3 | 46414714 | rs1249868905 | C | CTA | 1526.36 | PASS | TA | frameshift_variant | CCR5 | ENSG00000160791 | ENST00000445772.1:c.323_324dupAT |
| 3 | 46414774 | rs1372217574 | C | G | 950.36 | PASS | G | stop_gained | CCR5 | ENSG00000160791 | ENST00000292303.4:c.381C>G |
| 3 | 46414774 | rs1372217574 | C | G | 950.36 | PASS | G | stop_gained | CCR5 | ENSG00000160791 | ENST00000343801.4:c.381C>G |
| 3 | 46414774 | rs1372217574 | C | G | 950.36 | PASS | G | stop_gained | CCR5 | ENSG00000160791 | ENST00000445772.1:c.381C>G |
| 3 | 46414791 | rs1215591945 | CTG | C | 1355.36 | PASS | - | frameshift_variant | CCR5 | ENSG00000160791 | ENST00000292303.4:c.402_403delGT |
| 3 | 46414791 | rs1215591945 | CTG | C | 1355.36 | PASS | - | frameshift_variant | CCR5 | ENSG00000160791 | ENST00000343801.4:c.402_403delGT |
| 3 | 46414791 | rs1215591945 | CTG | C | 1355.36 | PASS | - | frameshift_variant | CCR5 | ENSG00000160791 | ENST00000445772.1:c.402_403delGT |
| 3 | 46414909 | rs1188964664 | AG | A | 712.37 | PASS | - | frameshift_variant | CCR5 | ENSG00000160791 | ENST00000292303.4:c.518delG |
| 3 | 46414909 | rs1188964664 | AG | A | 712.37 | PASS | - | frameshift_variant | CCR5 | ENSG00000160791 | ENST00000343801.4:c.518delG |
| 3 | 46414909 | rs1188964664 | AG | A | 712.37 | PASS | - | frameshift_variant | CCR5 | ENSG00000160791 | ENST00000445772.1:c.518delG |
| 3 | 46414935 | rs938517991 | AT | A | 9974.16 | PASS | - | frameshift_variant | CCR5 | ENSG00000160791 | ENST00000292303.4:c.546delT |
| 3 | 46414935 | rs938517991 | AT | A | 9974.16 | PASS | - | frameshift_variant | CCR5 | ENSG00000160791 | ENST00000343801.4:c.546delT |
| 3 | 46414935 | rs938517991 | AT | A | 9974.16 | PASS | - | frameshift_variant | CCR5 | ENSG00000160791 | ENST00000445772.1:c.546delT |
| 3 | 46414943 | rs775750898 | TACAGTCAGTATCAATTCTGGAAGAATTTCCAG | T | 74264261.52 | PASS | - | frameshift_variant | CCR5 | ENSG00000160791 | ENST00000292303.4:c.554_585delGTCAGTATCAATTCTGGAAGAATTTCCAGACA |
| 3 | 46414943 | rs775750898 | TACAGTCAGTATCAATTCTGGAAGAATTTCCAG | T | 74264261.52 | PASS | - | frameshift_variant | CCR5 | ENSG00000160791 | ENST00000343801.4:c.554_585delGTCAGTATCAATTCTGGAAGAATTTCCAGACA |
| 3 | 46414943 | rs775750898 | TACAGTCAGTATCAATTCTGGAAGAATTTCCAG | T | 74264261.52 | PASS | - | frameshift_variant | CCR5 | ENSG00000160791 | ENST00000445772.1:c.554_585delGTCAGTATCAATTCTGGAAGAATTTCCAGACA |
| 3 | 46414945 | rs746626584 | C | G | 74247720.02 | PASS | G | stop_gained | CCR5 | ENSG00000160791 | ENST00000292303.4:c.552C>G |
| 3 | 46414945 | rs746626584 | C | G | 74247720.02 | PASS | G | stop_gained | CCR5 | ENSG00000160791 | ENST00000343801.4:c.552C>G |
| 3 | 46414945 | rs746626584 | C | G | 74247720.02 | PASS | G | stop_gained | CCR5 | ENSG00000160791 | ENST00000445772.1:c.552C>G |
| 3 | 46414949 | rs113869679 | C | T | 74238735.71 | PASS | T | stop_gained | CCR5 | ENSG00000160791 | ENST00000292303.4:c.556C>T |
| 3 | 46414949 | rs113869679 | C | T | 74238735.71 | PASS | T | stop_gained | CCR5 | ENSG00000160791 | ENST00000343801.4:c.556C>T |
| 3 | 46414949 | rs113869679 | C | T | 74238735.71 | PASS | T | stop_gained | CCR5 | ENSG00000160791 | ENST00000445772.1:c.556C>T |
| 3 | 46415066 | rs146972949 | C | T | 120238.89 | PASS | T | stop_gained | CCR5 | ENSG00000160791 | ENST00000292303.4:c.673C>T |
| 3 | 46415066 | rs146972949 | C | T | 120238.89 | PASS | T | stop_gained | CCR5 | ENSG00000160791 | ENST00000343801.4:c.673C>T |
| 3 | 46415066 | rs146972949 | C | T | 120238.89 | PASS | T | stop_gained | CCR5 | ENSG00000160791 | ENST00000445772.1:c.673C>T |
| 3 | 46415168 | rs910924386 | AC | A | 156.36 | PASS | - | frameshift_variant | CCR5 | ENSG00000160791 | ENST00000292303.4:c.777delC |
| 3 | 46415168 | rs910924386 | AC | A | 156.36 | PASS | - | frameshift_variant | CCR5 | ENSG00000160791 | ENST00000343801.4:c.777delC |
| 3 | 46415168 | rs910924386 | AC | A | 156.36 | PASS | - | frameshift_variant | CCR5 | ENSG00000160791 | ENST00000445772.1:c.777delC |
| 3 | 46415174 | rs775289875 | C | T | 8429.37 | PASS | T | stop_gained | CCR5 | ENSG00000160791 | ENST00000292303.4:c.781C>T |
| 3 | 46415174 | rs775289875 | C | T | 8429.37 | PASS | T | stop_gained | CCR5 | ENSG00000160791 | ENST00000343801.4:c.781C>T |
| 3 | 46415174 | rs775289875 | C | T | 8429.37 | PASS | T | stop_gained | CCR5 | ENSG00000160791 | ENST00000445772.1:c.781C>T |
| 3 | 46415177 | rs1446832405 | G | T | 700.38 | PASS | T | stop_gained | CCR5 | ENSG00000160791 | ENST00000292303.4:c.784G>T |
| 3 | 46415177 | rs1446832405 | G | T | 700.38 | PASS | T | stop_gained | CCR5 | ENSG00000160791 | ENST00000343801.4:c.784G>T |
| 3 | 46415177 | rs1446832405 | G | T | 700.38 | PASS | T | stop_gained | CCR5 | ENSG00000160791 | ENST00000445772.1:c.784G>T |
| 3 | 46415238 | rs1294154353 | CAG | C | 1387.53 | PASS | - | frameshift_variant | CCR5 | ENSG00000160791 | ENST00000292303.4:c.849_850delGA |
| 3 | 46415238 | rs1294154353 | CAG | C | 1387.53 | PASS | - | frameshift_variant | CCR5 | ENSG00000160791 | ENST00000343801.4:c.849_850delGA |
| 3 | 46415238 | rs1294154353 | CAG | C | 1387.53 | PASS | - | frameshift_variant | CCR5 | ENSG00000160791 | ENST00000445772.1:c.849_850delGA |
| 3 | 46415271 | rs774050135 | AC | A | 10605.94 | PASS | - | frameshift_variant | CCR5 | ENSG00000160791 | ENST00000292303.4:c.882delC |
| 3 | 46415271 | rs774050135 | AC | A | 10605.94 | PASS | - | frameshift_variant | CCR5 | ENSG00000160791 | ENST00000343801.4:c.882delC |
| 3 | 46415271 | rs774050135 | AC | A | 10605.94 | PASS | - | frameshift_variant | CCR5 | ENSG00000160791 | ENST00000445772.1:c.882delC |
| 3 | 46414434 | rs758662716 | AT | A | 296.46 | PASS | - | frameshift_variant | CCR5 | ENSG00000160791 | ENST00000292303.4:c.43delT |
| 3 | 46414434 | rs758662716 | AT | A | 296.46 | PASS | - | frameshift_variant | CCR5 | ENSG00000160791 | ENST00000343801.4:c.43delT |
| 3 | 46414434 | rs758662716 | AT | A | 296.46 | PASS | - | frameshift_variant | CCR5 | ENSG00000160791 | ENST00000445772.1:c.43delT |
| 3 | 46414696 | rs1800560 | T | A | 16687.73 | PASS | A | stop_gained | CCR5 | ENSG00000160791 | ENST00000292303.4:c.303T>A |
| 3 | 46414696 | rs1800560 | T | A | 16687.73 | PASS | A | stop_gained | CCR5 | ENSG00000160791 | ENST00000343801.4:c.303T>A |
| 3 | 46414696 | rs1800560 | T | A | 16687.73 | PASS | A | stop_gained | CCR5 | ENSG00000160791 | ENST00000445772.1:c.303T>A |
| 3 | 46414943 | rs775750898 | TACAGTCAGTATCAATTCTGGAAGAATTTCCAG | T | 1947603.90 | PASS | - | frameshift_variant | CCR5 | ENSG00000160791 | ENST00000292303.4:c.554_585delGTCAGTATCAATTCTGGAAGAATTTCCAGACA |
| 3 | 46414943 | rs775750898 | TACAGTCAGTATCAATTCTGGAAGAATTTCCAG | T | 1947603.90 | PASS | - | frameshift_variant | CCR5 | ENSG00000160791 | ENST00000343801.4:c.554_585delGTCAGTATCAATTCTGGAAGAATTTCCAGACA |
| 3 | 46414943 | rs775750898 | TACAGTCAGTATCAATTCTGGAAGAATTTCCAG | T | 1947603.90 | PASS | - | frameshift_variant | CCR5 | ENSG00000160791 | ENST00000445772.1:c.554_585delGTCAGTATCAATTCTGGAAGAATTTCCAGACA |
| 3 | 46414949 | rs113869679 | C | T | 1942568.40 | PASS | T | stop_gained | CCR5 | ENSG00000160791 | ENST00000292303.4:c.556C>T |
| 3 | 46414949 | rs113869679 | C | T | 1942568.40 | PASS | T | stop_gained | CCR5 | ENSG00000160791 | ENST00000343801.4:c.556C>T |
| 3 | 46414949 | rs113869679 | C | T | 1942568.40 | PASS | T | stop_gained | CCR5 | ENSG00000160791 | ENST00000445772.1:c.556C>T |
| 3 | 46415066 | rs146972949 | C | T | 3449.38 | PASS | T | stop_gained | CCR5 | ENSG00000160791 | ENST00000292303.4:c.673C>T |
| 3 | 46415066 | rs146972949 | C | T | 3449.38 | PASS | T | stop_gained | CCR5 | ENSG00000160791 | ENST00000343801.4:c.673C>T |
| 3 | 46415066 | rs146972949 | C | T | 3449.38 | PASS | T | stop_gained | CCR5 | ENSG00000160791 | ENST00000445772.1:c.673C>T |
| 3 | 105243261 | rs1401656526 | T | TAATGC | 3920.14 | PASS | AATGC | frameshift_variant | ALCAM | ENSG00000170017 | ENST00000306107.5:c.306_310dupTGCAA |
| 3 | 105243261 | rs1401656526 | T | TAATGC | 3920.14 | PASS | AATGC | frameshift_variant | ALCAM | ENSG00000170017 | ENST00000472644.2:c.306_310dupTGCAA |
| 3 | 105243261 | rs1401656526 | T | TAATGC | 3920.14 | PASS | AATGC | frameshift_variant | ALCAM | ENSG00000170017 | ENST00000486979.2:c.153_157dupTGCAA |
| 3 | 105243324 | rs748382272 | TG | T | 3638.37 | PASS | - | frameshift_variant | ALCAM | ENSG00000170017 | ENST00000306107.5:c.367delG |
| 3 | 105243324 | rs748382272 | TG | T | 3638.37 | PASS | - | frameshift_variant | ALCAM | ENSG00000170017 | ENST00000472644.2:c.367delG |
| 3 | 105243324 | rs748382272 | TG | T | 3638.37 | PASS | - | frameshift_variant | ALCAM | ENSG00000170017 | ENST00000486979.2:c.214delG |
| 3 | 105252448 | rs763351683 | TG | T | 904.36 | PASS | - | frameshift_variant&splice_region_variant | ALCAM | ENSG00000170017 | ENST00000306107.5:c.464delG |
| 3 | 105252448 | rs763351683 | TG | T | 904.36 | PASS | - | frameshift_variant | ALCAM | ENSG00000170017 | ENST00000465413.2:c.6delG |
| 3 | 105252448 | rs763351683 | TG | T | 904.36 | PASS | - | frameshift_variant&splice_region_variant | ALCAM | ENSG00000170017 | ENST00000472644.2:c.464delG |
| 3 | 105252448 | rs763351683 | TG | T | 904.36 | PASS | - | frameshift_variant&splice_region_variant | ALCAM | ENSG00000170017 | ENST00000486979.2:c.311delG |
| 3 | 105253574 | rs753626110 | GGAGTACAA | G | 26588.50 | PASS | - | frameshift_variant | ALCAM | ENSG00000170017 | ENST00000306107.5:c.618_625delGTACAAGA |
| 3 | 105253574 | rs753626110 | GGAGTACAA | G | 26588.50 | PASS | - | frameshift_variant | ALCAM | ENSG00000170017 | ENST00000389927.4:c.45_52delGTACAAGA |
| 3 | 105253574 | rs753626110 | GGAGTACAA | G | 26588.50 | PASS | - | frameshift_variant | ALCAM | ENSG00000170017 | ENST00000465413.2:c.160_167delGTACAAGA |
| 3 | 105253574 | rs753626110 | GGAGTACAA | G | 26588.50 | PASS | - | frameshift_variant | ALCAM | ENSG00000170017 | ENST00000472644.2:c.618_625delGTACAAGA |
| 3 | 105253574 | rs753626110 | GGAGTACAA | G | 26588.50 | PASS | - | frameshift_variant | ALCAM | ENSG00000170017 | ENST00000486979.2:c.465_472delGTACAAGA |
| 3 | 105258923 | rs1409380546 | G | T | 230.36 | PASS | T | stop_gained | ALCAM | ENSG00000170017 | ENST00000306107.5:c.835G>T |
| 3 | 105258923 | rs1409380546 | G | T | 230.36 | PASS | T | stop_gained | ALCAM | ENSG00000170017 | ENST00000472644.2:c.835G>T |
| 3 | 105258923 | rs1409380546 | G | T | 230.36 | PASS | T | stop_gained | ALCAM | ENSG00000170017 | ENST00000486979.2:c.682G>T |
| 3 | 105266064 | rs748308492 | C | A | 7063.46 | PASS | A | stop_gained | ALCAM | ENSG00000170017 | ENST00000306107.5:c.1176C>A |
| 3 | 105266064 | rs748308492 | C | A | 7063.46 | PASS | A | stop_gained | ALCAM | ENSG00000170017 | ENST00000389927.4:c.342C>A |
| 3 | 105266064 | rs748308492 | C | A | 7063.46 | PASS | A | stop_gained | ALCAM | ENSG00000170017 | ENST00000465413.2:c.457C>A |
| 3 | 105266064 | rs748308492 | C | A | 7063.46 | PASS | A | stop_gained | ALCAM | ENSG00000170017 | ENST00000472644.2:c.1176C>A |
| 3 | 105266064 | rs748308492 | C | A | 7063.46 | PASS | A | stop_gained | ALCAM | ENSG00000170017 | ENST00000486979.2:c.1023C>A |
| 3 | 105266100 | rs1189829981 | AAG | A | 54.42 | PASS | - | frameshift_variant | ALCAM | ENSG00000170017 | ENST00000306107.5:c.1217_1218delAG |
| 3 | 105266100 | rs1189829981 | AAG | A | 54.42 | PASS | - | frameshift_variant | ALCAM | ENSG00000170017 | ENST00000389927.4:c.383_384delAG |
| 3 | 105266100 | rs1189829981 | AAG | A | 54.42 | PASS | - | frameshift_variant | ALCAM | ENSG00000170017 | ENST00000465413.2:c.498_499delAG |
| 3 | 105266100 | rs1189829981 | AAG | A | 54.42 | PASS | - | frameshift_variant | ALCAM | ENSG00000170017 | ENST00000472644.2:c.1217_1218delAG |
| 3 | 105266100 | rs1189829981 | AAG | A | 54.42 | PASS | - | frameshift_variant | ALCAM | ENSG00000170017 | ENST00000486979.2:c.1064_1065delAG |
| 3 | 105266129 | rs1165397359 | G | T | 244.57 | PASS | T | splice_donor_variant | ALCAM | ENSG00000170017 | ENST00000306107.5:c.1240+1G>T |
| 3 | 105266129 | rs1165397359 | G | T | 244.57 | PASS | T | splice_donor_variant | ALCAM | ENSG00000170017 | ENST00000389927.4:c.406+1G>T |
| 3 | 105266129 | rs1165397359 | G | T | 244.57 | PASS | T | splice_donor_variant | ALCAM | ENSG00000170017 | ENST00000465413.2:c.521+1G>T |
| 3 | 105266129 | rs1165397359 | G | T | 244.57 | PASS | T | splice_donor_variant | ALCAM | ENSG00000170017 | ENST00000472644.2:c.1240+1G>T |
| 3 | 105266129 | rs1165397359 | G | T | 244.57 | PASS | T | splice_donor_variant | ALCAM | ENSG00000170017 | ENST00000486979.2:c.1087+1G>T |
| 3 | 105268977 | . | G | T | 273.40 | PASS | T | stop_gained | ALCAM | ENSG00000170017 | ENST00000306107.5:c.1381G>T |
| 3 | 105268977 | . | G | T | 273.40 | PASS | T | stop_gained | ALCAM | ENSG00000170017 | ENST00000389927.4:c.547G>T |
| 3 | 105268977 | . | G | T | 273.40 | PASS | T | stop_gained | ALCAM | ENSG00000170017 | ENST00000465413.2:c.662G>T |
| 3 | 105268977 | . | G | T | 273.40 | PASS | T | stop_gained | ALCAM | ENSG00000170017 | ENST00000472644.2:c.1381G>T |
| 3 | 105268977 | . | G | T | 273.40 | PASS | T | stop_gained | ALCAM | ENSG00000170017 | ENST00000486979.2:c.1228G>T |
| 3 | 105270986 | rs1249936676 | A | G | 151.43 | PASS | G | splice_acceptor_variant | ALCAM | ENSG00000170017 | ENST00000306107.5:c.1508-2A>G |
| 3 | 105270986 | rs1249936676 | A | G | 151.43 | PASS | G | splice_acceptor_variant | ALCAM | ENSG00000170017 | ENST00000389927.4:c.674-2A>G |
| 3 | 105270986 | rs1249936676 | A | G | 151.43 | PASS | G | splice_acceptor_variant | ALCAM | ENSG00000170017 | ENST00000465413.2:c.789-2A>G |
| 3 | 105270986 | rs1249936676 | A | G | 151.43 | PASS | G | splice_acceptor_variant | ALCAM | ENSG00000170017 | ENST00000486979.2:c.1355-2A>G |
| 3 | 105270987 | rs764096754 | G | A | 1329.70 | PASS | A | splice_acceptor_variant | ALCAM | ENSG00000170017 | ENST00000306107.5:c.1508-1G>A |
| 3 | 105270987 | rs764096754 | G | A | 1329.70 | PASS | A | splice_acceptor_variant | ALCAM | ENSG00000170017 | ENST00000389927.4:c.674-1G>A |
| 3 | 105270987 | rs764096754 | G | A | 1329.70 | PASS | A | splice_acceptor_variant | ALCAM | ENSG00000170017 | ENST00000465413.2:c.789-1G>A |
| 3 | 105270987 | rs764096754 | G | A | 1329.70 | PASS | A | splice_acceptor_variant | ALCAM | ENSG00000170017 | ENST00000486979.2:c.1355-1G>A |
| 3 | 105252445 | rs1264516297 | A | T | 208.47 | PASS | T | splice_acceptor_variant | ALCAM | ENSG00000170017 | ENST00000306107.5:c.460-2A>T |
| 3 | 105252445 | rs1264516297 | A | T | 208.47 | PASS | T | splice_acceptor_variant | ALCAM | ENSG00000170017 | ENST00000472644.2:c.460-2A>T |
| 3 | 105252445 | rs1264516297 | A | T | 208.47 | PASS | T | splice_acceptor_variant | ALCAM | ENSG00000170017 | ENST00000486979.2:c.307-2A>T |