Case usage in the SynMall feature module. (A) Workflow for feature extraction from a given variant call format (VCF) file. (1) Select the molecular category: DNA, RNA, or protein. (2) Choose feature types to compute. (3) Upload the VCF file. (4) Specify the sequence context length and reference genome version. (B) DNA-level features distinguishing functional sSNVs. (C) RNA-level features distinguishing functional sSNVs. (D) Protein-level features distinguishing functional sSNVs. (PseKRAAC) Pseudo K-tuple-reduced amino acid composition. (E) UMAP visualization of SpliceBERT embeddings with a 129-bp window. (F) UMAP visualization of GPN-MSA embeddings with a 129-bp window. (G) UMAP visualization of ERNIE-RNA embeddings with a 129-bp window. (H) UMAP visualization of ISM embeddings with a 43-amino-acid window. (Reference) Embeddings of the reference sequence surrounding the mutation, (alternate) embeddings of the alternate sequence, (difference) alternate minus reference embeddings.