# hg38: run of 15 A's from chr9:133,269,985-133,269,999
# HGVS insertion on the right, forward strand of genome:
NC_000009.12:g.133269999_133270000insA
NC_000009.12:g.133269999_133270000insAAAA
NC_000009.12:g.133269999_133270000insAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
# Deletions
NC_000009.12:g.133269999del
NC_000009.12:g.133269990_133269999del
# This should not be shifted:
NC_000009.12:g.133269984_133269999del
# NM_020469.2(ABO) utr3 exon has run of 5 AC's on - strand; GT on + chr9:133,255,436-133,255,445
NC_000009.12:g.133255445_133255446insGT
NC_000009.12:g.133255445_133255446insGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT
NC_000009.12:g.133255445_133255446del
# This should not be shifted:
NC_000009.12:g.133255445_133255447del

# NM_020469.2(ABO) utr3 exon has run of 5 AC's on - strand; GT on + chr9:133,255,436-133,255,445
# 000001309 tcacacacacacc 000001321
# <<<<<<<<< ||||||||||||| <<<<<<<<<
# 133255447 tcacacacacacc 133255435
# The repeat range in NM_020469.2 mRNA coords is (1-based) 1310 - 1319
# HGVS UTR3 coords are relative to cdsEnd which is 1090 for NM_020469.2.
# Subtracting 1090, the c. coords of the repeat region are (1-based) 220 - 229.
# This actually needs to be shifted right one base because there is a C after all the CACA:
NM_020469.3:c.*229_*230insCA
# This is properly right-shifted on NM_020469.2, so due to strand-swapping it is
# already left-shifted on the genome and does not need to be left-shifted for VCF:
NM_020469.3:c.*230_*231insAC
# But somebody might forego right-alignment on NM_020469.2, meaning we would
# need to left-shift on the genome for VCF:
NM_020469.3:c.*221_*222insCA
NM_020469.3:c.*220_*221insAC
NM_020469.3:c.*219_*220insCA

# Try indels at (or shiftable to) the beginning of a chrom.  chr9 begins with Ns.
# What are the proper HGVS coordinates for insertion at the beginning of a sequence?
NC_000009.12:g.1del
NC_000009.12:g.2del
NC_000009.12:g.10000del
NC_000009.12:g.1_10del
NC_000009.12:g.2_11del
NC_000009.12:g.1_2insN
NC_000009.12:g.1_2insNNNNNNNNNNNNNNNN
NC_000009.12:g.2_3insN
# These are not shiftable.
NC_000009.12:g.1_2insA
NC_000009.12:g.1_2insAAAAAAAAAAAAAAAA
NC_000009.12:g.2_3insA