Skip to main content

Table 1 Exemplar variants demonstrating nomenclature discrepancies

From: A variant by any name: quantifying annotation discordance across tools and clinical databases

  ClinVar COSMIC SnpEff Vep VR Preferred HGVS Reference ID
Coding HGVS: variant type        
Insertion   c.2339_2340insGGGCTCCCC c.2331_2339dupGGGCTCCCC c.2331_2339dupGGGCTCCCC   c.2331_2339dup COSM12555*
Insertion - c.2262_2263ins14 - c.2262_2263insGGCATCTCAGCATC - c.2262_2263insGGCATCTCAGCATC COSM5254274
Deletion c.1200-1delG   c.1200delG c.1200delG c.1201delAinsGA c.1200-1delG PTV021, rs63186960
Deletion c.1895 + 1_1895 + 4delGTGA   c.1895 + 5_1895 + 8delGTGA c.1895 + 5_1895 + 8delGTGA c.1895 + 9GTGAC > C c.1895 + 5_1895 + 8delGTGA PTV003, rs386834023
Duplication - c.422_423insA c.428dupA c.428dupA - c.428dup COSM4719972
Indel - c.3141_3142GA > TT c.3141_3142delGAinsTT c.3141_3142delGAinsTT - c.3141_3142delinsTT COSM4387531
Indel c.68-5_68-3delinsTT - c.68-5_68-3delCTCinsTT c.68-5_68-3delCTCinsTT c.68-5_68-3delCTCinsTT c.68-5_68-3delinsTT rs397516362
SNV c.1621A=   c.1621A>G c.1621A>G c.1621G= c.1621G= PTV099, rs2228006
Protein HGVS: consequence        
Frameshift p.Arg227Lysfs - p.Arg227fs p.Arg227LysfsTer31 - All are acceptable rs80356649
Frameshift - p.P1176fs*>46 p.Pro1176fs p.Pro1176AlafsTer117 - p.Pro1176fs or p.Pro1176AlafsTer117 COSM5196763
Frameshift - - p.Glu238fs p.Glu238ProfsTer9 p.Phe237_Glu238insPro p.Glu238fs or p.Glu238ProfsTer9 PTV009
In-frame insertion - p.Pro780_Tyr781insGlySerPro p.Pro780_Tyr781insGlySerPro p.Gly778_Pro780dup - p.Gly778_Pro780dup COSM125551
Synonymous p.Arg317= - p.Arg317Arg p.= p.Arg317= p.Arg317= rs111033272
Synonymous - p.*1143* p.Ter1143Ter p.= - p.Ter1143= COSM3558732
Stop gained p.Gln100Ter - p.Gln100* p.Gln100Ter - All are acceptable rs119103276
Extention - p.*1133L p.Ter1133Leuext*? p.Ter1133LeuextTer22 - p.Ter1133LeuextTer22 COSM1569676
In-frame insertion - - p.Arg309_Arg310insArgArg p.Arg310_Arg311dup p.Arg311_Lys312insArgArg p.Arg310_Arg311dup PTV082
In-frame insertion - p.T502_H505delTTGH p.Thr502_His505del p.Thr502_His505del - p.Thr502_His505del COSM1163654
In-frame deletion - - p.Ala1111_Ala1119del p.Ala1111_Ala1119del p.Ala1119_Gly1120insAlaAlaAlaAlaAlaAlaAlaAlaAla p.Ala1111_Ala1119del PTV021
  1. 1 Known in My Cancer Genome as “G778_P780dup”