Laboratory Medicine and Quality Assurance

Table. 1.

Variant nomenclature changed based on the results of variant call format normalization

Chr Position Ref Alt Gene Transcript Pre-normalization GATK LAATV vt-normalize Validation
chr5 74021847 ACTCAAA A PYGL NM_001281302.1 c.1921_1926delTTTGAG c.1922_1927delTTGAGT c.1922_1927delTTGAGT No
chr14 51375699 TA TAA PIEZO1 NM_002863.4 c.2178-28dupT c.2178-27dupT c.2178-27dupT No
chr16 88793089 CA CG PIEZO1 NM_001142864.2 c.3699+33T>C c.3699+33T>C c.3699+33_3699+ 34delTGinsCC No
chr18 67863851 C CTCC RTTN NM_173630.3 c.724_726dupGGA c.725_727dupGAG c.725_727dupGAG Yes
chr2 179634391 TATT TT TTN NM_001267550.1 c.8902+13_8902+ 14delAT c.8902+28_8902+ 29delTA c.8902+13_8902+ 14delAT No
chr6 65016997 AGA A EYS NM_001142800.1 c.6079-24_6079- 23delTC c.6079-4_6079-3delTC c.6079-4_6079-3delTC No
chr6 70983674 ATAAA A COL9A1 NM_001851.4 c.1065+72_1065+ 75delTTTA c.1065+102_1065+ 105delTATT c.1065+102_1065+ 105delTATT No
chr11 86658278 ACAA A FZD4 NM_012193.3 c.*3903_*3905delTTG c.*3908_*3910delGTT c.*3908_*3910delGTT No
chrX 31165667 AAAAGAAAGAA AAAAGAA DMD NM_004006.2 c.10554-42_10554- 39delTTCT c.10554-36_10554- 33delCTTT c.10554-36_10554- 33delCTTT No

Abbreviations: Chr, chromosome; Ref, reference allele; Alt, alternative allele; GATK, Genome Analysis Toolkit; LAATV, LeftAlignAndTrimVariants.

Lab Med Qual Assur 2022;44:212~215 https://doi.org/10.15263/jlmqa.2022.44.4.212
© Lab Med Qual Assur