I found some very important variants without genetic model annotations using genmod. I have checked, however, I can't to get the reason.
Some variants in vcf are:
chr19 39914146 . C G 620.16 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=1.58;ClippingRankSum=0;DP=78;ExcessHet=3.9794;FS=2.425;MLEAC=2;MLEAF=0.333;MQ=60;MQRankSum=0;QD=12.66;ReadPosRankSum=0.724;SOR=0.694;CSQ=G|missense_variant|MODERATE|PLEKHG2|64857|Transcript|NM_022835.2|protein_coding|18/19||NM_022835.2:c.2452C>G|NP_073746.2:p.Arg818Gly|2777|2452|818|R/G|Cga/Gga|rs758449222&COSM3224027&COSM3224028&COSM3224029||1||EntrezGene|||||C|C|OK|||deleterious_low_confidence(0)|probably_damaging(0.924)||chr19:g.39914146C>G|||||||||0|0|0|0|0|0|0|0|0||gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS||0&1&1&1|0&1&1&1|||||||;ALLELE_END;Annotation=PLEKHG2 GT:AD:DP:GQ:PGT:PID:PL 0/1:17,8:25:99:0|1:39914132_C_T:254,0,465 0/1:8,16:24:99:0|1:39914146_C_G:398,0,194 0/0:28,0:28:81:.:.:0,81,931
chr1 12837764 . C G 362.16 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=1.51;ClippingRankSum=0;DP=89;ExcessHet=3.9794;FS=1.326;MLEAC=2;MLEAF=0.333;MQ=58.13;MQRankSum=-1.924;QD=6.24;ReadPosRankSum=0.297;SOR=0.358;CSQ=G|3_prime_UTR_variant|MODIFIER|PRAMEF12|390999|Transcript|NM_001080830.1|protein_coding|3/3||NM_001080830.1:c.*22C>G||1501|||||rs141977389||1||EntrezGene||YES|||C|C|||||||chr1:g.12837764C>G|||||||0.00227|0.01012|0.006704|0.001144|0.003838|0.006718|0.006312|0.006331|0.006931|0.00661|0.01275|0.01275|gnomAD_SAS|||||||||chr1:12837764-12837764|0.0344;ALLELE_END;Annotation=PRAMEF12 GT:AD:DP:GQ:PL 0/1:24,8:32:99:212,0,735 0/1:17,9:26:99:182,0,528 0/0:27,0:27:60:0,60,900
I found some very important variants without genetic model annotations using genmod. I have checked, however, I can't to get the reason.
Some variants in vcf are: chr19 39914146 . C G 620.16 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=1.58;ClippingRankSum=0;DP=78;ExcessHet=3.9794;FS=2.425;MLEAC=2;MLEAF=0.333;MQ=60;MQRankSum=0;QD=12.66;ReadPosRankSum=0.724;SOR=0.694;CSQ=G|missense_variant|MODERATE|PLEKHG2|64857|Transcript|NM_022835.2|protein_coding|18/19||NM_022835.2:c.2452C>G|NP_073746.2:p.Arg818Gly|2777|2452|818|R/G|Cga/Gga|rs758449222&COSM3224027&COSM3224028&COSM3224029||1||EntrezGene|||||C|C|OK|||deleterious_low_confidence(0)|probably_damaging(0.924)||chr19:g.39914146C>G|||||||||0|0|0|0|0|0|0|0|0||gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS||0&1&1&1|0&1&1&1|||||||;ALLELE_END;Annotation=PLEKHG2 GT:AD:DP:GQ:PGT:PID:PL 0/1:17,8:25:99:0|1:39914132_C_T:254,0,465 0/1:8,16:24:99:0|1:39914146_C_G:398,0,194 0/0:28,0:28:81:.:.:0,81,931 chr1 12837764 . C G 362.16 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=1.51;ClippingRankSum=0;DP=89;ExcessHet=3.9794;FS=1.326;MLEAC=2;MLEAF=0.333;MQ=58.13;MQRankSum=-1.924;QD=6.24;ReadPosRankSum=0.297;SOR=0.358;CSQ=G|3_prime_UTR_variant|MODIFIER|PRAMEF12|390999|Transcript|NM_001080830.1|protein_coding|3/3||NM_001080830.1:c.*22C>G||1501|||||rs141977389||1||EntrezGene||YES|||C|C|||||||chr1:g.12837764C>G|||||||0.00227|0.01012|0.006704|0.001144|0.003838|0.006718|0.006312|0.006331|0.006931|0.00661|0.01275|0.01275|gnomAD_SAS|||||||||chr1:12837764-12837764|0.0344;ALLELE_END;Annotation=PRAMEF12 GT:AD:DP:GQ:PL 0/1:24,8:32:99:212,0,735 0/1:17,9:26:99:182,0,528 0/0:27,0:27:60:0,60,900