The first 34 columns are standard MAF format, and described here:
https://wiki.nci.nih.gov/x/eJaPAQ

The subsequent 10 columns are relevant to most analyses.

35. HGVSc - the coding sequence of the variant in HGVS recommended format
36. HGVSp - the protein sequence of the variant in HGVS recommended format
37. HGVSp_Short - Same as HGVSp, but using 1-letter amino-acid codes
38. Transcript_ID - transcript onto which the consequence of the variant has been mapped
39. Exon_Number - the exon number (out of total number)
40. t_depth - read depth across this locus in tumor BAM
41. t_ref_count - read depth supporting the reference allele in tumor BAM
42. t_alt_count - read depth supporting the variant allele in tumor BAM
43. n_depth - read depth across this locus in normal BAM
44. n_ref_count - read depth supporting the reference allele in normal BAM
45. n_alt_count - read depth supporting the variant allele in normal BAM

The next column is relevant to analyses that consider the effect of the variant on all alternate
isoforms of the gene, or on non-coding/regulatory transcripts. The effects are sorted first by
transcript biotype priority, then by effect severity, and finally by decreasing order of transcript
length. Each effect in the list is in the format [SYMBOL,Consequence,HGVSp,Transcript_ID].

46. all_effects - a semicolon delimited list of all possible variant effects, sorted by priority

All remaining columns are straight out of Ensembl's VEP annotator, as described here:
http://useast.ensembl.org/info/docs/tools/vep/vep_formats.html#output

47. Allele - the variant allele used to calculate the consequence
48. Gene - stable Ensembl ID of affected gene
49. Feature - stable Ensembl ID of feature
50. Feature_type - type of feature. Currently one of Transcript, RegulatoryFeature, MotifFeature
51. Consequence - consequence type of this variation
52. cDNA_position - relative position of base pair in cDNA sequence
53. CDS_position - relative position of base pair in coding sequence
54. Protein_position - relative position of amino acid in protein
55. Amino_acids - only given if the variation affects the protein-coding sequence
56. Codons - the alternative codons with the variant base in upper case
57. Existing_variation - known identifier of existing variation
58. ALLELE_NUM - allele number from input; 0 is reference, 1 is first alternate etc
59. DISTANCE - shortest distance from variant to transcript
60. STRAND - the DNA strand (1 or -1) on which the transcript/feature lies
61. SYMBOL - the gene symbol
62. SYMBOL_SOURCE - the source of the gene symbol
63. HGNC_ID - gene identifier from the HUGO Gene Nomenclature Committee
64. BIOTYPE - biotype of transcript
65. CANONICAL - a flag indicating if the transcript is denoted as the canonical transcript for this gene
66. CCDS - the CCDS identifer for this transcript, where applicable
67. ENSP - the Ensembl protein identifier of the affected transcript
68. SWISSPROT - UniProtKB/Swiss-Prot identifier of protein product
69. TREMBL - UniProtKB/TrEMBL identifier of protein product
70. UNIPARC - UniParc identifier of protein product
71. RefSeq - RefSeq identifier for this transcript
72. SIFT - the SIFT prediction and/or score, with both given as prediction (score)
73. PolyPhen - the PolyPhen prediction and/or score
74. EXON - the exon number (out of total number)
75. INTRON - the intron number (out of total number)
76. DOMAINS - the source and identifer of any overlapping protein domains
77. GMAF - minor allele and frequency of existing variation in 1000 Genomes Phase 1
78. AFR_MAF - minor allele and frequency of existing variation in 1000 Genomes Phase 1 combined African population
79. AMR_MAF - minor allele and frequency of existing variation in 1000 Genomes Phase 1 combined American population
80. ASN_MAF - minor allele and frequency of existing variation in 1000 Genomes Phase 1 combined Asian population
81. EUR_MAF - minor allele and frequency of existing variation in 1000 Genomes Phase 1 combined European population
82. AA_MAF - minor allele and frequency of existing variant in NHLBI-ESP African American population
83. EA_MAF - minor allele and frequency of existing variant in NHLBI-ESP European American population
84. CLIN_SIG - clinical significance of variant from dbSNP
85. SOMATIC - somatic status of existing variation(s)
86. PUBMED - pubmed ID(s) of publications that cite existing variant
87. MOTIF_NAME - the source and identifier of a transcription factor binding profile aligned at this position
88. MOTIF_POS - the relative position of the variation in the aligned TFBP
89. HIGH_INF_POS - a flag indicating if the variant falls in a high information position of a transcription factor binding profile (TFBP)
90. MOTIF_SCORE_CHANGE - the difference in motif score of the reference and variant sequences for the TFBP
