## ENSEMBL VARIANT EFFECT PREDICTOR format (UCSC Variant Annotation Integrator) ## Connected to UCSC database hg19 ## Variants: indelTrimVcf (input/annoGrator/indelTrim.vcf) ## Transcripts: EnsemblGenes ... (hg19.wgEncodeGencodeBasicV19) Uploaded Variation Location Allele Gene Feature Feature type Consequence Position in cDNA Position in CDS Position in protein Amino acid change Codon change Co-located Variation Extra indel chr11:373409-373410 - B4GALNT4 ENST00000329962.6 Transcript intron_variant - - - - - - INTRON=6/19 indel chr11:373409-373410 C B4GALNT4 ENST00000329962.6 Transcript intron_variant - - - - - - INTRON=6/19 indel chr11:1905147 - LSP1 ENST00000311604.3 Transcript splice_region_variant - - - - - - INTRON=4/10 indel chr11:1905147 TT LSP1 ENST00000311604.3 Transcript splice_region_variant - - - - - - INTRON=4/10 indel chr11:1905147 - LSP1 ENST00000381775.1 Transcript splice_region_variant - - - - - - INTRON=5/11 indel chr11:1905147 TT LSP1 ENST00000381775.1 Transcript splice_region_variant - - - - - - INTRON=5/11 indel chr11:1905147 - LSP1 ENST00000405957.2 Transcript splice_region_variant - - - - - - INTRON=4/10 indel chr11:1905147 TT LSP1 ENST00000405957.2 Transcript splice_region_variant - - - - - - INTRON=4/10 indel chr11:1905147 - LSP1 ENST00000406638.2 Transcript splice_region_variant - - - - - - INTRON=4/10 indel chr11:1905147 TT LSP1 ENST00000406638.2 Transcript splice_region_variant - - - - - - INTRON=4/10 indel chr11:1905147 - LSP1 ENST00000485341.1 Transcript splice_region_variant - - - - - - INTRON=3/9 indel chr11:1905147 TT LSP1 ENST00000485341.1 Transcript splice_region_variant - - - - - - INTRON=3/9 indel chr11:6411931-6411942 CTGGCG SMPD1 ENST00000356761.2 Transcript inframe_deletion 281-286 107-112 36 VL/- gTGCTGGcg/gcg - EXON=1/5 indel chr11:6411931-6411942 - SMPD1 ENST00000356761.2 Transcript inframe_deletion 281-292 107-118 36 VLAL/- gTGCTGGCGCTGGcg/gcg - EXON=1/5 indel chr11:6411931-6411942 CTGGCG SMPD1 ENST00000299397.3 Transcript inframe_deletion 281-286 107-112 36 VL/- gTGCTGGcg/gcg - EXON=1/5 indel chr11:6411931-6411942 - SMPD1 ENST00000299397.3 Transcript inframe_deletion 281-292 107-118 36 VLAL/- gTGCTGGCGCTGGcg/gcg - EXON=1/5 indel chr11:6411931-6411942 CTGGCG SMPD1 ENST00000342245.4 Transcript inframe_deletion 275-280 107-112 36 VL/- gTGCTGGcg/gcg - EXON=1/6 indel chr11:6411931-6411942 - SMPD1 ENST00000342245.4 Transcript inframe_deletion 275-286 107-118 36 VLAL/- gTGCTGGCGCTGGcg/gcg - EXON=1/6 indel chr11:6411931-6411942 CTGGCG SMPD1 ENST00000533196.1 Transcript non_coding_transcript_exon_variant 266-271 - - - - - EXON=1/2 indel chr11:6411931-6411942 - SMPD1 ENST00000533196.1 Transcript non_coding_transcript_exon_variant 266-277 - - - - - EXON=1/2 indel chr11:6411931-6411942 CTGGCG SMPD1 ENST00000527275.1 Transcript inframe_deletion 231-236 107-112 36 VL/- gTGCTGGcg/gcg - EXON=1/6 indel chr11:6411931-6411942 - SMPD1 ENST00000527275.1 Transcript inframe_deletion 231-242 107-118 36 VLAL/- gTGCTGGCGCTGGcg/gcg - EXON=1/6 indel chr11:6411931-6411942 CTGGCG APBB1 ENST00000526240.1 Transcript downstream_gene_variant - - - - - - DISTANCE=4424 indel chr11:6411931-6411942 - APBB1 ENST00000526240.1 Transcript downstream_gene_variant - - - - - - DISTANCE=4424 indel chr11:6411931-6411942 CTGGCG APBB1 ENST00000608655.1 Transcript downstream_gene_variant - - - - - - DISTANCE=4424 indel chr11:6411931-6411942 - APBB1 ENST00000608655.1 Transcript downstream_gene_variant - - - - - - DISTANCE=4424 indel chr11:6411931-6411942 CTGGCG APBB1 ENST00000608704.1 Transcript downstream_gene_variant - - - - - - DISTANCE=4424 indel chr11:6411931-6411942 - APBB1 ENST00000608704.1 Transcript downstream_gene_variant - - - - - - DISTANCE=4424 indel chr11:6411931-6411942 CTGGCG APBB1 ENST00000299402.6 Transcript downstream_gene_variant - - - - - - DISTANCE=4424 indel chr11:6411931-6411942 - APBB1 ENST00000299402.6 Transcript downstream_gene_variant - - - - - - DISTANCE=4424 indel chr11:6411931-6411942 CTGGCG APBB1 ENST00000609360.1 Transcript downstream_gene_variant - - - - - - DISTANCE=4424 indel chr11:6411931-6411942 - APBB1 ENST00000609360.1 Transcript downstream_gene_variant - - - - - - DISTANCE=4424 indel chr11:6411931-6411942 CTGGCG APBB1 ENST00000389906.2 Transcript downstream_gene_variant - - - - - - DISTANCE=4424 indel chr11:6411931-6411942 - APBB1 ENST00000389906.2 Transcript downstream_gene_variant - - - - - - DISTANCE=4424 indel chr11:6411931-6411942 CTGGCG APBB1 ENST00000311051.3 Transcript downstream_gene_variant - - - - - - DISTANCE=4424 indel chr11:6411931-6411942 - APBB1 ENST00000311051.3 Transcript downstream_gene_variant - - - - - - DISTANCE=4424 indel chr11:6411931-6411942 CTGGCG APBB1 ENST00000608394.1 Transcript downstream_gene_variant - - - - - - DISTANCE=4442 indel chr11:6411931-6411942 - APBB1 ENST00000608394.1 Transcript downstream_gene_variant - - - - - - DISTANCE=4442 indel chr11:6411931-6411942 CTGGCG APBB1 ENST00000529519.1 Transcript downstream_gene_variant - - - - - - DISTANCE=4462 indel chr11:6411931-6411942 - APBB1 ENST00000529519.1 Transcript downstream_gene_variant - - - - - - DISTANCE=4462 indel chr11:6411931-6411942 CTGGCG APBB1 ENST00000608645.1 Transcript downstream_gene_variant - - - - - - DISTANCE=4603 indel chr11:6411931-6411942 - APBB1 ENST00000608645.1 Transcript downstream_gene_variant - - - - - - DISTANCE=4603 indel chr11:6411931-6411942 CTGGCG APBB1 ENST00000609331.1 Transcript downstream_gene_variant - - - - - - DISTANCE=4729 indel chr11:6411931-6411942 - APBB1 ENST00000609331.1 Transcript downstream_gene_variant - - - - - - DISTANCE=4729 indel chr11:6411931-6411942 CTGGCG APBB1 ENST00000530885.1 Transcript downstream_gene_variant - - - - - - DISTANCE=4767 indel chr11:6411931-6411942 - APBB1 ENST00000530885.1 Transcript downstream_gene_variant - - - - - - DISTANCE=4767 indel chr11:6637740-6637742 TT TAF10 ENST00000299424.4 Transcript upstream_gene_variant - - - - - - DISTANCE=3842 indel chr11:6637740-6637742 - TAF10 ENST00000299424.4 Transcript upstream_gene_variant - - - - - - DISTANCE=3842 indel chr11:6637740-6637742 T TAF10 ENST00000299424.4 Transcript upstream_gene_variant - - - - - - DISTANCE=3842 indel chr11:6637740-6637742 TT TAF10 ENST00000531760.1 Transcript upstream_gene_variant - - - - - - DISTANCE=3970 indel chr11:6637740-6637742 - TAF10 ENST00000531760.1 Transcript upstream_gene_variant - - - - - - DISTANCE=3970 indel chr11:6637740-6637742 T TAF10 ENST00000531760.1 Transcript upstream_gene_variant - - - - - - DISTANCE=3970 indel chr11:6637740-6637742 TT TPP1 ENST00000299427.6 Transcript splice_region_variant - - - - - - INTRON=7/12 indel chr11:6637740-6637742 - TPP1 ENST00000299427.6 Transcript splice_region_variant - - - - - - INTRON=7/12 indel chr11:6637740-6637742 T TPP1 ENST00000299427.6 Transcript splice_region_variant - - - - - - INTRON=7/12 indel chr11:6637740-6637742 TT TPP1 ENST00000533371.1 Transcript splice_region_variant - - - - - - INTRON=6/11 indel chr11:6637740-6637742 - TPP1 ENST00000533371.1 Transcript splice_region_variant - - - - - - INTRON=6/11 indel chr11:6637740-6637742 T TPP1 ENST00000533371.1 Transcript splice_region_variant - - - - - - INTRON=6/11 indel chr11:6637740-6637742 TT TPP1 ENST00000534644.1 Transcript downstream_gene_variant - - - - - - DISTANCE=502 indel chr11:6637740-6637742 - TPP1 ENST00000534644.1 Transcript downstream_gene_variant - - - - - - DISTANCE=502 indel chr11:6637740-6637742 T TPP1 ENST00000534644.1 Transcript downstream_gene_variant - - - - - - DISTANCE=502 indel chr11:6637740-6637742 TT TPP1 ENST00000528657.1 Transcript downstream_gene_variant - - - - - - DISTANCE=2220 indel chr11:6637740-6637742 - TPP1 ENST00000528657.1 Transcript downstream_gene_variant - - - - - - DISTANCE=2220 indel chr11:6637740-6637742 T TPP1 ENST00000528657.1 Transcript downstream_gene_variant - - - - - - DISTANCE=2220 indel chr11:6637740-6637742 TT RP11-732A19.9 ENST00000545572.1 Transcript upstream_gene_variant - - - - - - DISTANCE=2281 indel chr11:6637740-6637742 - RP11-732A19.9 ENST00000545572.1 Transcript upstream_gene_variant - - - - - - DISTANCE=2281 indel chr11:6637740-6637742 T RP11-732A19.9 ENST00000545572.1 Transcript upstream_gene_variant - - - - - - DISTANCE=2281 indel chr11:6637740-6637742 TT DCHS1 ENST00000299441.3 Transcript downstream_gene_variant - - - - - - DISTANCE=4816 indel chr11:6637740-6637742 - DCHS1 ENST00000299441.3 Transcript downstream_gene_variant - - - - - - DISTANCE=4816 indel chr11:6637740-6637742 T DCHS1 ENST00000299441.3 Transcript downstream_gene_variant - - - - - - DISTANCE=4816 indel chr11:6637740-6637742 TT RP11-732A19.5 ENST00000526456.1 Transcript upstream_gene_variant - - - - - - DISTANCE=4942 indel chr11:6637740-6637742 - RP11-732A19.5 ENST00000526456.1 Transcript upstream_gene_variant - - - - - - DISTANCE=4942 indel chr11:6637740-6637742 T RP11-732A19.5 ENST00000526456.1 Transcript upstream_gene_variant - - - - - - DISTANCE=4942 indel chr11:56128673-56128674 TA OR8J1 ENST00000303039.3 Transcript 3_prime_UTR_variant 984-985 - - - - - EXON=1/1 indel chr11:56128673-56128674 T OR8J1 ENST00000303039.3 Transcript 3_prime_UTR_variant 987-988 - - - - - EXON=1/1 indel chr11:85979637-85979638 GTGT EED ENST00000263360.6 Transcript intron_variant - - - - - - INTRON=9/11 indel chr11:85979637-85979638 GTGTGTGT EED ENST00000263360.6 Transcript intron_variant - - - - - - INTRON=9/11 indel chr11:85979637-85979638 GTGTGTGTGT EED ENST00000263360.6 Transcript intron_variant - - - - - - INTRON=9/11 indel chr11:85979637-85979638 - EED ENST00000263360.6 Transcript intron_variant - - - - - - INTRON=9/11 indel chr11:85979637-85979638 GTGTGT EED ENST00000263360.6 Transcript intron_variant - - - - - - INTRON=9/11 indel chr11:85979637-85979638 GTGT EED ENST00000528180.1 Transcript intron_variant - - - - - - INTRON=7/9 indel chr11:85979637-85979638 GTGTGTGT EED ENST00000528180.1 Transcript intron_variant - - - - - - INTRON=7/9 indel chr11:85979637-85979638 GTGTGTGTGT EED ENST00000528180.1 Transcript intron_variant - - - - - - INTRON=7/9 indel chr11:85979637-85979638 - EED ENST00000528180.1 Transcript intron_variant - - - - - - INTRON=7/9 indel chr11:85979637-85979638 GTGTGT EED ENST00000528180.1 Transcript intron_variant - - - - - - INTRON=7/9 indel chr11:85979637-85979638 GTGT EED ENST00000327320.4 Transcript intron_variant - - - - - - INTRON=9/10 indel chr11:85979637-85979638 GTGTGTGT EED ENST00000327320.4 Transcript intron_variant - - - - - - INTRON=9/10 indel chr11:85979637-85979638 GTGTGTGTGT EED ENST00000327320.4 Transcript intron_variant - - - - - - INTRON=9/10 indel chr11:85979637-85979638 - EED ENST00000327320.4 Transcript intron_variant - - - - - - INTRON=9/10 indel chr11:85979637-85979638 GTGTGT EED ENST00000327320.4 Transcript intron_variant - - - - - - INTRON=9/10 indel chr11:85979637-85979638 GTGT EED ENST00000351625.6 Transcript intron_variant - - - - - - INTRON=9/12 indel chr11:85979637-85979638 GTGTGTGT EED ENST00000351625.6 Transcript intron_variant - - - - - - INTRON=9/12 indel chr11:85979637-85979638 GTGTGTGTGT EED ENST00000351625.6 Transcript intron_variant - - - - - - INTRON=9/12 indel chr11:85979637-85979638 - EED ENST00000351625.6 Transcript intron_variant - - - - - - INTRON=9/12 indel chr11:85979637-85979638 GTGTGT EED ENST00000351625.6 Transcript intron_variant - - - - - - INTRON=9/12 indelASH chr11:85979637-85979638 GTGT EED ENST00000263360.6 Transcript intron_variant - - - - - - INTRON=9/11 indelASH chr11:85979637-85979638 GTGTGTGT EED ENST00000263360.6 Transcript intron_variant - - - - - - INTRON=9/11 indelASH chr11:85979637-85979638 GTGTGTGTGT EED ENST00000263360.6 Transcript intron_variant - - - - - - INTRON=9/11 indelASH chr11:85979637-85979638 - EED ENST00000263360.6 Transcript intron_variant - - - - - - INTRON=9/11 indelASH chr11:85979637-85979638 GTGTGT EED ENST00000263360.6 Transcript intron_variant - - - - - - INTRON=9/11 indelASH chr11:85979637-85979638 GTGT EED ENST00000528180.1 Transcript intron_variant - - - - - - INTRON=7/9 indelASH chr11:85979637-85979638 GTGTGTGT EED ENST00000528180.1 Transcript intron_variant - - - - - - INTRON=7/9 indelASH chr11:85979637-85979638 GTGTGTGTGT EED ENST00000528180.1 Transcript intron_variant - - - - - - INTRON=7/9 indelASH chr11:85979637-85979638 - EED ENST00000528180.1 Transcript intron_variant - - - - - - INTRON=7/9 indelASH chr11:85979637-85979638 GTGTGT EED ENST00000528180.1 Transcript intron_variant - - - - - - INTRON=7/9 indelASH chr11:85979637-85979638 GTGT EED ENST00000327320.4 Transcript intron_variant - - - - - - INTRON=9/10 indelASH chr11:85979637-85979638 GTGTGTGT EED ENST00000327320.4 Transcript intron_variant - - - - - - INTRON=9/10 indelASH chr11:85979637-85979638 GTGTGTGTGT EED ENST00000327320.4 Transcript intron_variant - - - - - - INTRON=9/10 indelASH chr11:85979637-85979638 - EED ENST00000327320.4 Transcript intron_variant - - - - - - INTRON=9/10 indelASH chr11:85979637-85979638 GTGTGT EED ENST00000327320.4 Transcript intron_variant - - - - - - INTRON=9/10 indelASH chr11:85979637-85979638 GTGT EED ENST00000351625.6 Transcript intron_variant - - - - - - INTRON=9/12 indelASH chr11:85979637-85979638 GTGTGTGT EED ENST00000351625.6 Transcript intron_variant - - - - - - INTRON=9/12 indelASH chr11:85979637-85979638 GTGTGTGTGT EED ENST00000351625.6 Transcript intron_variant - - - - - - INTRON=9/12 indelASH chr11:85979637-85979638 - EED ENST00000351625.6 Transcript intron_variant - - - - - - INTRON=9/12 indelASH chr11:85979637-85979638 GTGTGT EED ENST00000351625.6 Transcript intron_variant - - - - - - INTRON=9/12 indel chr11:89914894-89914898 - NAALAD2 ENST00000534061.1 Transcript intron_variant - - - - - - INTRON=17/18 indel chr11:89914894-89914898 - NAALAD2 ENST00000321955.4 Transcript intron_variant - - - - - - INTRON=16/17 indel chr11:89914894-89914898 - NAALAD2 ENST00000375944.3 Transcript intron_variant - - - - - - INTRON=6/6 indelASH chr11:89914894-89914898 - NAALAD2 ENST00000534061.1 Transcript intron_variant - - - - - - INTRON=17/18 indelASH chr11:89914894-89914898 - NAALAD2 ENST00000321955.4 Transcript intron_variant - - - - - - INTRON=16/17 indelASH chr11:89914894-89914898 - NAALAD2 ENST00000375944.3 Transcript intron_variant - - - - - - INTRON=6/6 indel chr11:107686741-107686742 AC SLC35F2 ENST00000525815.1 Transcript intron_variant - - - - - - INTRON=1/7 indel chr11:107686741-107686742 AC SLC35F2 ENST00000525071.1 Transcript intron_variant - - - - - - INTRON=4/10 indel chr11:107686741-107686742 AC SLC35F2 ENST00000265836.7 Transcript intron_variant - - - - - - INTRON=1/6 indel chr11:107686741-107686742 AC SLC35F2 ENST00000375682.4 Transcript intron_variant - - - - - - INTRON=1/7 indel chr11:107686741-107686742 AC SLC35F2 ENST00000429869.1 Transcript intron_variant - - - - - - INTRON=4/10 indelASH chr11:107686741-107686742 AC SLC35F2 ENST00000525815.1 Transcript intron_variant - - - - - - INTRON=1/7 indelASH chr11:107686741-107686742 AC SLC35F2 ENST00000525071.1 Transcript intron_variant - - - - - - INTRON=4/10 indelASH chr11:107686741-107686742 AC SLC35F2 ENST00000265836.7 Transcript intron_variant - - - - - - INTRON=1/6 indelASH chr11:107686741-107686742 AC SLC35F2 ENST00000375682.4 Transcript intron_variant - - - - - - INTRON=1/7 indelASH chr11:107686741-107686742 AC SLC35F2 ENST00000429869.1 Transcript intron_variant - - - - - - INTRON=4/10 snp chr11:108014662 A ACAT1 ENST00000265838.4 Transcript intron_variant - - - - - - INTRON=9/11 snp chr11:108014684 G ACAT1 ENST00000265838.4 Transcript intron_variant - - - - - - INTRON=9/11 duff chr11:125452300-125452301 C EI24 ENST00000530985.1 Transcript non_coding_transcript_exon_variant 1275-1276 - - - - - EXON=10/11 duff chr11:125452300-125452301 C EI24 ENST00000343678.4 Transcript inframe_insertion 977-978 735-736 246 -/L -/CTG - EXON=9/10 duff chr11:125452300-125452301 C EI24 ENST00000278903.6 Transcript inframe_insertion 1085-1086 843-844 282 -/T -/ACC - EXON=10/11 duff chr11:125452300-125452301 - EI24 ENST00000278903.6 Transcript frameshift_variant 1085-1086 843-844 282 PGKAY...TAGH*(59 aa)/TLAKHISSSCASSPWWSS* cctggcaaagca...gcaggtcactga(177 nt)/ACcctggcaaag...tggtcttcttaa(57 nt) - EXON=10/11 duff chr11:125452300-125452301 C STT3A-AS1 ENST00000530526.1 Transcript intron_variant - - - - - - INTRON=1/2 duff chr11:125452300-125452301 C STT3A-AS1 ENST00000532714.1 Transcript intron_variant - - - - - - INTRON=1/1 duffASH chr11:125452300-125452301 C EI24 ENST00000530985.1 Transcript non_coding_transcript_exon_variant 1275-1276 - - - - - EXON=10/11 duffASH chr11:125452300-125452301 C EI24 ENST00000343678.4 Transcript inframe_insertion 977-978 735-736 246 -/L -/CTG - EXON=9/10 duffASH chr11:125452300-125452301 C EI24 ENST00000278903.6 Transcript inframe_insertion 1085-1086 843-844 282 -/T -/ACC - EXON=10/11 duffASH chr11:125452300-125452301 - EI24 ENST00000278903.6 Transcript frameshift_variant 1085-1086 843-844 282 PGKAY...TAGH*(59 aa)/TLAKHISSSCASSPWWSS* cctggcaaagca...gcaggtcactga(177 nt)/ACcctggcaaag...tggtcttcttaa(57 nt) - EXON=10/11 duffASH chr11:125452300-125452301 C STT3A-AS1 ENST00000530526.1 Transcript intron_variant - - - - - - INTRON=1/2 duffASH chr11:125452300-125452301 C STT3A-AS1 ENST00000532714.1 Transcript intron_variant - - - - - - INTRON=1/1