I downloaded the data from Breast Invasive Carcinoma (TCGA, PanCancer Atlas) from cBioPortal and this is the mutation you're referring to:
Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Hotspot AA_MAF AFR_MAF ALLELE_NUM AMR_MAF ASN_MAF Allele Amino_acids BIOTYPE CANONICAL CCDS CDS_position CENTERS CLIN_SIG CONTEXT COSMIC DBVS DISTANCE DOMAINS EAS_MAF EA_MAF ENSP EUR_MAF EXON ExAC_AF ExAC_AF_AFR ExAC_AF_AMR ExAC_AF_EAS ExAC_AF_FIN ExAC_AF_NFE ExAC_AF_OTH ExAC_AF_SAS Existing_variation FILTER Feature Feature_type GENE_PHENO GMAF Gene HGNC_ID HGVS_OFFSET HIGH_INF_POS IMPACT INTRON MERGESOURCE MOTIF_NAME MOTIF_POS MOTIF_SCORE_CHANGE NCALLERS PHENO PICK PolyPhen SAS_MAF SIFT SOMATIC SWISSPROT SYMBOL SYMBOL_SOURCE TREMBL TSL UNIPARC VARIANT_CLASS all_effects cDNA_position n_depth t_depth Annotation_Status
HINT3 135114 . GRCh37 6 126299011 126299011 + 3_prime_UTR_variant 3'UTR SNP T T A novel . TCGA-A8-A09A-01 TCGA-A8-A09A-10 T T . . . . . . . . . . . . . 29 16 60 0 ENST00000229633.5:c.*189T>A ENST00000229633 NM_138571.4 0 . . . . . A . protein_coding YES CCDS5133.1 . RADIA|MUTECT|MUSE . GTTACTGACTT NONE . . . . . ENSP00000229633 . 5/5 . . . . . . . . . wga ENST00000229633 Transcript . . ENSG00000111911 18468 . . MODIFIER . PRIMARY . . . 3 . . . . . . HINT3_HUMAN HINT3 HGNC . . UPI000006F73F SNV HINT3,3_prime_UTR_variant,,ENST00000229633,;RNA5SP216,downstream_gene_variant,,ENST00000516111,; 935 60 46 SUCCESS
As you can see, the consequence type is "3_prime_UTR_variant". You can find information on mutation consequence classification here.
From cBioPortal FAQ:
Does the cBioPortal contain synonymous mutation data?
No, the cBioPortal does not currently support synonymous mutations. This may change in the future, but we have no plans yet to add this feature.
You can read about it in more detail in this discussion and also this one, but basically, as explained here cBioPortal filters out "synonymous" mutations (Silent, Intron, IGR, 3'UTR, 5'UTR, 3'Flank and 5'Flank), as it is assumed that these will have no impact on the patient.
In fact, if you see the list of mutated genes for this patient in cBioPortal , you can see that the only mutation types are "Frame_Shift_Del", "In_Frame_Del", "Missense_Mutation", "Nonsense_Mutation" and "Splice_Region". If you filter the original data that you can download from cBioPortal to only include these mutation types, you get 191 unique genes out of the 289 unique genes with any mutations, close to the 199 unique genes appearing as mutated on cBioPortal. I suspect the overlap isn't identical because they use different gene aliases for the differing genes (HS6ST2, XRCC6BP1, FAM214A, HKR1, KIAA0947, AIM1 are only in original data; ATOSA, ATP23, CLEC4D, COG3, CRYBG1, FNBP1L, HNMT, ICE1, LOXL4, MRPL45, RCBTB1, SEMA7A, ST6GAL1, ZNF875 are only in cBioPortal).
If for some reason you want to include these synonymous mutations into your analysis, then I suggest you use GDC Data Portal, which lets you filter mutations based on genes, types and predicted impact. Keep in mind the data might not be the same (some samples might have been excluded in the PanCancer version) and the pipeline used to call the mutations is different (GDC uses an ensemble of 4 methods and I'm not sure what PanCancer used). For example, for the patient you mentioned there are only 221 somatic mutations on the GDC Data Portal, and HINT3 isn't among them; it does show a CNV loss for HINT3, interestingly.
