I want to count values/word occurrence in second and third column of a tab delim txt file, where first column value is same

Input file:

```
GeneA Pathogenic snp
GeneA Pathogenic snp
GeneA Benign indel
GeneA Likely_pathogenic snp
GeneA Pathogenic    indel
GeneB Benign    snp
GeneB Pathogenic    snp
GeneB Benign    indel
GeneC  Benign   snp
GeneC  Likely_pathogenic    snp

```

Expected Output:(tabular format)

```
| Pathogenic | Benign | Likely_Pathogenic | snp | indel |
 ------------|--------|-------------------|-----|-------|
|GeneA|     3|       1|                  1|    3|      2|
|GeneB|     1|       2|                  0|    2|      1|
|GeneC|     0|       1|                  1|    2|      0|

```