synonymous mutation reported as insertion by GEMINI

[Shantanu Kumar]

Input Variant annotated by VEP:

chr10    89717712    COSM5822    CG    CA    90.7692    PASS    AF=0.0336345;AO=380;DP=12294;FAO=67;FDP=1992;FR=.;FRO=1925;FSAF=35;FSAR=32;FSRF=967;FSRR=958;FWDB=0.010404;FXX=0.00399998;HRUN=1;LEN=1;MLLD=182.706;OALT=-,A,T;OID=COSM5822,.,COSM5111;OMAPALT=C,CA,TG;OPOS=89717713,89717713,89717712;OREF=G,G,C;QD=0.182268;RBI=0.0686884;REFB=1.41821e-05;REVB=-0.0678959;RO=11728;SAF=184;SAR=196;SRF=5895;SRR=5833;SSEN=0;SSEP=0;SSSB=-0.0145713;STB=0.519375;STBP=0.766;TYPE=snp;VARB=-0.000588148;HS;CSQ=CA|synonymous_variant|LOW|PTEN|ENSG00000171862|Transcript|ENST00000371953|protein_coding|7/9||ENST00000371953.3:c.738delinsA|ENSP00000361021.3:p.Pro246%3D|2094-2095/9027|737-738/1212|246/403|cCG/cCA|P|||CCDS31238.1|||1|||YES||||||||||||||||||||||    GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR    0/1:91:12294:1992:11728:1925:2,380,4:0,67,0:0,0.0336345,0:1,196,3:1,184,1:5895:5833:0,32,0:0,35,0:967:958

Variant reported by GEMINI

chr10    89717711    89717713    CG    CA    90.769203186    indel    ins    -1.0    0    None    0    None    None    None    acute_megakaryoblastic_leukemia|bannayan-riley-ruvalcaba_syndrome|cowden_syndrome|cowden_syndrome_1|endometrial_carcinoma|glioma_susceptibility_2|hereditary_cancer-predisposing_syndrome|inborn_genetic_diseases|lhermitte-duclos_disease|macrocephaly/autism_syndrome|malignant_melanoma|mediastinal_germ_cell_tumor|meningioma|pten_hamartoma_tumor_syndrome|prostate_cancer\x2c_somatic|proteus-like_syndrome|squamous_cell_carcinoma_of_the_head_and_neck|tumor_susceptibility_linked_to_germline_bap1_mutations|vater_association_with_macrocephaly_and_ventriculomegaly    None    chr10q23.31    0    0    1    None    3.32956e-213    0    1    0    0.5    PTEN    ENST00000371953    1    1    0    07/9    cCG/cCA    P    246/403    synonymous_variant    LOW        None        None    12294    None    None    None    None    None    None    0    -1.0    -1.0    -1.0    0    -1.0    -1.0    -1.0    -1.0    -1.0    -1.0    None    None    None    0    -1.0    -1.0    -1.0    -1.0    -1.0    -1.0    -1.0    -1.0    -1.0    ENST00000371953.3:c.738delinsA    ENSP00000361021.3:p.Pro246%3D    2094-2095/9027    737-738/1212    1                                                                    NA    CG/CA    1    91.0    11728    386    12114

Observation:

1. Input is synonymous mutation, output as insertion by GEMINI

2. If type is indel/ins , the consequence reported by GEMINI is synonymous_variant

[Brent Pedersen]

Hi, can you share a VCF that contains just this variant and the header?
That will help me debug this issue.
-Brent

[Brent Pedersen]

By they way CG -> CA is just G -> C, so it looks like VEP is noting
that and calling it a synonymous variant.