Transcript analysis identifies low levels of canonical splice products associated with the c.3624C>T variant. (A) Traces of Sanger sequencing from 64 cloned reverse transcription PCR products amplified from region around FANCA exon 36 using RNA derived from RA2349 fibroblasts. Two of 64 clones exhibited normal spliced product at the splice donor site of exon 36 with the synonymous variant present. The remaining 62 clones showed a 4-bp deletion. (B) Schematic of the qf-PCR method used for relative quantification of splice products at exon 36-37 junction. (C) qf-PCR peak profiles showing that 6% to 10% of products had normal splicing. The average peak amplitude from 3 independent experiments was used to calculate relative percentage of product(s). (D) Integrative Genomics Viewer showing MiSeq deep sequencing of the c.3624C>T variant position in RA2349 cell line. Low-level expression of the normally spliced product. (E) Number of reads and percentages at each indicated position from MiSeq analysis of 3 cell lines including fibroblast RA2349 and 2 lymphoblastoid cell lines, RA2219 and RA2140, all derived from individual 2.