gnomADe annotation not presented for a variant

[Aisha-D]

Describe the issue

A variant (X:15823107C>CAGCCGG) was not annotated using the gnomADe VCF provided (r2.1.1) by VEP b38. The gnomADe VCF has this variant present with AF=0.0147404 and so should have annotated the variant with the correct information :

chrX	15823107	rs752736259	C	CAGCCGG	3697473.05	PASS	AC=2495;AC_afr=566;AC_afr_female=464;AC_afr_male=102;AC_amr=168;AC_amr_female=139;AC_amr_male=29;AC_asj=339;AC_asj_female=256;AC_asj_male=83;AC_eas=11;AC_eas_female=10;AC_eas_jpn=0;AC_eas_kor=4;AC_eas_male=1;AC_eas_oea=7;AC_female=1882;AC_fin=382;AC_fin_female=271;AC_fin_male=111;AC_male=613;AC_nfe=904;AC_nfe_bgr=28;AC_nfe_est=1;AC_nfe_female=669;AC_nfe_male=235;AC_nfe_nwe=391;AC_nfe_onf=270;AC_nfe_seu=71;AC_nfe_swe=143;AC_oth=55;AC_oth_female=41;AC_oth_male=14;AC_popmax=566;AC_raw=3148;AC_sas=70;AC_sas_female=32;AC_sas_male=38;AF=1.47404e-02;AF_afr=5.26316e-02;AF_afr_female=5.58498e-02;AF_afr_male=4.17007e-02;AF_amr=6.32673e-03;AF_amr_female=6.94653e-03;AF_amr_male=4.43154e-03;AF_asj=4.80306e-02;AF_asj_female=5.44449e-02;AF_asj_male=3.52292e-02;AF_eas=8.35930e-04;AF_eas_female=1.09890e-03;AF_eas_jpn=0.00000e+00;AF_eas_kor=1.40154e-03;AF_eas_male=2.46366e-04;AF_eas_oea=6.84530e-04;AF_female=1.72111e-02;AF_fin=2.49624e-02;AF_fin_female=2.66104e-02;AF_fin_male=2.16839e-02;AF_male=1.02312e-02;AF_nfe=1.22568e-02;AF_nfe_bgr=1.57392e-02;AF_nfe_est=5.74713e-03;AF_nfe_female=1.43059e-02;AF_nfe_male=8.70661e-03;AF_nfe_nwe=1.36071e-02;AF_nfe_onf=1.33988e-02;AF_nfe_seu=1.25909e-02;AF_nfe_swe=8.27690e-03;AF_oth=1.29503e-02;AF_oth_female=1.46953e-02;AF_oth_male=9.60879e-03;AF_popmax=5.26316e-02;AF_raw=1.72382e-02;AF_sas=3.79754e-03;AF_sas_female=4.27236e-03;AF_sas_male=3.47254e-03;AN=169263;AN_afr=10754;AN_afr_female=8308;AN_afr_male=2446;AN_amr=26554;AN_amr_female=20010;AN_amr_male=6544;AN_asj=7058;AN_asj_female=4702;AN_asj_male=2356;AN_eas=13159;AN_eas_female=9100;AN_eas_jpn=79;AN_eas_kor=2854;AN_eas_male=4059;AN_eas_oea=10226;AN_female=109348;AN_fin=15303;AN_fin_female=10184;AN_fin_male=5119;AN_male=59915;AN_nfe=73755;AN_nfe_bgr=1779;AN_nfe_est=174;AN_nfe_female=46764;AN_nfe_male=26991;AN_nfe_nwe=28735;AN_nfe_onf=20151;AN_nfe_seu=5639;AN_nfe_swe=17277;AN_oth=4247;AN_oth_female=2790;AN_oth_male=1457;AN_popmax=10754;AN_raw=182618;AN_sas=18433;AN_sas_female=7490;AN_sas_male=10943;BaseQRankSum=3.61000e-01;ClippingRankSum=6.70000e-02;DP=5725913;FS=5.43000e-01;InbreedingCoeff=4.49800e-01;MQ=5.51700e+01;MQRankSum=-1.58900e+00;OriginalContig=X;OriginalStart=15841230;QD=2.35500e+01;ReadPosRankSum=-4.19000e-01;SOR=6.50000e-01;VQSLOD=1.36000e+00;VQSR_culprit=FS;ab_hist_alt_bin_freq=1|1|12|8|35|116|237|320|548|376|418|178|127|51|17|33|41|50|31|3;age_hist_het_bin_freq=51|60|102|109|133|125|128|99|86|65;age_hist_het_n_larger=37;age_hist_het_n_smaller=68;age_hist_hom_bin_freq=10|19|35|48|63|43|50|37|30|19;age_hist_hom_n_larger=8;age_hist_hom_n_smaller=13;allele_type=ins;controls_AC=1096;controls_AC_afr=265;controls_AC_afr_female=217;controls_AC_afr_male=48;controls_AC_amr=90;controls_AC_amr_female=76;controls_AC_amr_male=14;controls_AC_asj=67;controls_AC_asj_female=59;controls_AC_asj_male=8;controls_AC_eas=6;controls_AC_eas_female=6;controls_AC_eas_jpn=0;controls_AC_eas_kor=2;controls_AC_eas_male=0;controls_AC_eas_oea=4;controls_AC_female=838;controls_AC_fin=269;controls_AC_fin_female=186;controls_AC_fin_male=83;controls_AC_male=258;controls_AC_nfe=354;controls_AC_nfe_bgr=8;controls_AC_nfe_est=1;controls_AC_nfe_female=269;controls_AC_nfe_male=85;controls_AC_nfe_nwe=139;controls_AC_nfe_onf=107;controls_AC_nfe_seu=24;controls_AC_nfe_swe=75;controls_AC_oth=15;controls_AC_oth_female=11;controls_AC_oth_male=4;controls_AC_popmax=265;controls_AC_raw=1356;controls_AC_sas=30;controls_AC_sas_female=14;controls_AC_sas_male=16;controls_AF=1.45570e-02;controls_AF_afr=5.24960e-02;controls_AF_afr_female=5.56125e-02;controls_AF_afr_male=4.18848e-02;controls_AF_amr=6.81096e-03;controls_AF_amr_female=7.53819e-03;controls_AF_amr_male=4.46999e-03;controls_AF_asj=4.10791e-02;controls_AF_asj_female=5.17544e-02;controls_AF_asj_male=1.62933e-02;controls_AF_eas=9.34871e-04;controls_AF_eas_female=1.30095e-03;controls_AF_eas_jpn=0.00000e+00;controls_AF_eas_kor=1.38026e-03;controls_AF_eas_male=0.00000e+00;controls_AF_eas_oea=8.13835e-04;controls_AF_female=1.69368e-02;controls_AF_fin=2.81175e-02;controls_AF_fin_female=2.93283e-02;controls_AF_fin_male=2.57364e-02;controls_AF_male=9.99535e-03;controls_AF_nfe=1.24407e-02;controls_AF_nfe_bgr=1.74292e-02;controls_AF_nfe_est=2.17391e-02;controls_AF_nfe_female=1.47268e-02;controls_AF_nfe_male=8.34233e-03;controls_AF_nfe_nwe=1.36448e-02;controls_AF_nfe_onf=1.57631e-02;controls_AF_nfe_seu=1.07817e-02;controls_AF_nfe_swe=8.57241e-03;controls_AF_oth=1.08696e-02;controls_AF_oth_female=1.15304e-02;controls_AF_oth_male=9.38967e-03;controls_AF_popmax=5.24960e-02;controls_AF_raw=1.69250e-02;controls_AF_sas=3.13250e-03;controls_AF_sas_female=3.34928e-03;controls_AF_sas_male=2.96461e-03;controls_AN=75290;controls_AN_afr=5048;controls_AN_afr_female=3902;controls_AN_afr_male=1146;controls_AN_amr=13214;controls_AN_amr_female=10082;controls_AN_amr_male=3132;controls_AN_asj=1631;controls_AN_asj_female=1140;controls_AN_asj_male=491;controls_AN_eas=6418;controls_AN_eas_female=4612;controls_AN_eas_jpn=54;controls_AN_eas_kor=1449;controls_AN_eas_male=1806;controls_AN_eas_oea=4915;controls_AN_female=49478;controls_AN_fin=9567;controls_AN_fin_female=6342;controls_AN_fin_male=3225;controls_AN_male=25812;controls_AN_nfe=28455;controls_AN_nfe_bgr=459;controls_AN_nfe_est=46;controls_AN_nfe_female=18266;controls_AN_nfe_male=10189;controls_AN_nfe_nwe=10187;controls_AN_nfe_onf=6788;controls_AN_nfe_seu=2226;controls_AN_nfe_swe=8749;controls_AN_oth=1380;controls_AN_oth_female=954;controls_AN_oth_male=426;controls_AN_popmax=5048;controls_AN_raw=80118;controls_AN_sas=9577;controls_AN_sas_female=4180;controls_AN_sas_male=5397;controls_nhomalt=13;controls_nhomalt_afr=4;controls_nhomalt_afr_female=4;controls_nhomalt_afr_male=0;controls_nhomalt_amr=1;controls_nhomalt_amr_female=1;controls_nhomalt_amr_male=0;controls_nhomalt_asj=3;controls_nhomalt_asj_female=3;controls_nhomalt_asj_male=0;controls_nhomalt_eas=0;controls_nhomalt_eas_female=0;controls_nhomalt_eas_jpn=0;controls_nhomalt_eas_kor=0;controls_nhomalt_eas_male=0;controls_nhomalt_eas_oea=0;controls_nhomalt_female=13;controls_nhomalt_fin=3;controls_nhomalt_fin_female=3;controls_nhomalt_fin_male=0;controls_nhomalt_male=0;controls_nhomalt_nfe=2;controls_nhomalt_nfe_bgr=0;controls_nhomalt_nfe_est=0;controls_nhomalt_nfe_female=2;controls_nhomalt_nfe_male=0;controls_nhomalt_nfe_nwe=1;controls_nhomalt_nfe_onf=1;controls_nhomalt_nfe_seu=0;controls_nhomalt_nfe_swe=0;controls_nhomalt_oth=0;controls_nhomalt_oth_female=0;controls_nhomalt_oth_male=0;controls_nhomalt_popmax=4;controls_nhomalt_raw=20;controls_nhomalt_sas=0;controls_nhomalt_sas_female=0;controls_nhomalt_sas_male=0;controls_popmax=afr;dp_hist_all_bin_freq=5541|11272|17213|19476|19779|15658|16569|27393|18172|6668|2565|1301|778|509|326|248|214|109|113|96;dp_hist_all_n_larger=331;dp_hist_alt_bin_freq=249|646|631|546|356|285|213|145|113|86|105|105|125|90|87|50|41|21|20|15;dp_hist_alt_n_larger=79;faf95=1.42582e-02;faf95_afr=4.90456e-02;faf95_amr=5.54570e-03;faf95_eas=4.68540e-04;faf95_nfe=1.15939e-02;faf95_sas=3.08274e-03;faf99=1.42575e-02;faf99_afr=4.90457e-02;faf99_amr=5.54547e-03;faf99_eas=4.68720e-04;faf99_nfe=1.15934e-02;faf99_sas=3.08262e-03;gq_hist_all_bin_freq=2637|4114|2531|5426|6806|3945|8248|8748|4623|8459|8219|4214|10294|4148|5388|4429|6651|1902|5844|56564;gq_hist_alt_bin_freq=12|91|109|132|180|118|104|123|99|69|74|66|45|37|24|39|37|26|33|2590;n_alt_alleles=6;nhomalt=32;nhomalt_afr=13;nhomalt_afr_female=13;nhomalt_afr_male=0;nhomalt_amr=1;nhomalt_amr_female=1;nhomalt_amr_male=0;nhomalt_asj=6;nhomalt_asj_female=6;nhomalt_asj_male=0;nhomalt_eas=0;nhomalt_eas_female=0;nhomalt_eas_jpn=0;nhomalt_eas_kor=0;nhomalt_eas_male=0;nhomalt_eas_oea=0;nhomalt_female=32;nhomalt_fin=6;nhomalt_fin_female=6;nhomalt_fin_male=0;nhomalt_male=0;nhomalt_nfe=6;nhomalt_nfe_bgr=1;nhomalt_nfe_est=0;nhomalt_nfe_female=6;nhomalt_nfe_male=0;nhomalt_nfe_nwe=2;nhomalt_nfe_onf=1;nhomalt_nfe_seu=0;nhomalt_nfe_swe=2;nhomalt_oth=0;nhomalt_oth_female=0;nhomalt_oth_male=0;nhomalt_popmax=13;nhomalt_raw=54;nhomalt_sas=0;nhomalt_sas_female=0;nhomalt_sas_male=0;non_cancer_AC=2379;non_cancer_AC_afr=524;non_cancer_AC_afr_female=427;non_cancer_AC_afr_male=97;non_cancer_AC_amr=166;non_cancer_AC_amr_female=137;non_cancer_AC_amr_male=29;non_cancer_AC_asj=332;non_cancer_AC_asj_female=249;non_cancer_AC_asj_male=83;non_cancer_AC_eas=11;non_cancer_AC_eas_female=10;non_cancer_AC_eas_jpn=0;non_cancer_AC_eas_kor=4;non_cancer_AC_eas_male=1;non_cancer_AC_eas_oea=7;non_cancer_AC_female=1785;non_cancer_AC_fin=382;non_cancer_AC_fin_female=271;non_cancer_AC_fin_male=111;non_cancer_AC_male=594;non_cancer_AC_nfe=843;non_cancer_AC_nfe_bgr=28;non_cancer_AC_nfe_est=1;non_cancer_AC_nfe_female=620;non_cancer_AC_nfe_male=223;non_cancer_AC_nfe_nwe=376;non_cancer_AC_nfe_onf=242;non_cancer_AC_nfe_seu=60;non_cancer_AC_nfe_swe=136;non_cancer_AC_oth=51;non_cancer_AC_oth_female=39;non_cancer_AC_oth_male=12;non_cancer_AC_popmax=524;non_cancer_AC_raw=2940;non_cancer_AC_sas=70;non_cancer_AC_sas_female=32;non_cancer_AC_sas_male=38;non_cancer_AF=1.48767e-02;non_cancer_AF_afr=5.33279e-02;non_cancer_AF_afr_female=5.64815e-02;non_cancer_AF_afr_male=4.28067e-02;non_cancer_AF_amr=6.30292e-03;non_cancer_AF_amr_female=6.90315e-03;non_cancer_AF_amr_male=4.46772e-03;non_cancer_AF_asj=4.93240e-02;non_cancer_AF_asj_female=5.60558e-02;non_cancer_AF_asj_male=3.62604e-02;non_cancer_AF_eas=8.66278e-04;non_cancer_AF_eas_female=1.14155e-03;non_cancer_AF_eas_jpn=0.00000e+00;non_cancer_AF_eas_kor=1.41443e-03;non_cancer_AF_eas_male=2.53936e-04;non_cancer_AF_eas_oea=7.13630e-04;non_cancer_AF_female=1.74225e-02;non_cancer_AF_fin=2.49836e-02;non_cancer_AF_fin_female=2.66418e-02;non_cancer_AF_fin_male=2.16882e-02;non_cancer_AF_male=1.03374e-02;non_cancer_AF_nfe=1.26324e-02;non_cancer_AF_nfe_bgr=1.65192e-02;non_cancer_AF_nfe_est=8.84956e-03;non_cancer_AF_nfe_female=1.48838e-02;non_cancer_AF_nfe_male=8.89261e-03;non_cancer_AF_nfe_nwe=1.39803e-02;non_cancer_AF_nfe_onf=1.49503e-02;non_cancer_AF_nfe_seu=1.18087e-02;non_cancer_AF_nfe_swe=8.11359e-03;non_cancer_AF_oth=1.29870e-02;non_cancer_AF_oth_female=1.51633e-02;non_cancer_AF_oth_male=8.85609e-03;non_cancer_AF_popmax=5.33279e-02;non_cancer_AF_raw=1.71456e-02;non_cancer_AF_sas=3.80994e-03;non_cancer_AF_sas_female=4.29761e-03;non_cancer_AF_sas_male=3.47762e-03;non_cancer_AN=159915;non_cancer_AN_afr=9826;non_cancer_AN_afr_female=7560;non_cancer_AN_afr_male=2266;non_cancer_AN_amr=26337;non_cancer_AN_amr_female=19846;non_cancer_AN_amr_male=6491;non_cancer_AN_asj=6731;non_cancer_AN_asj_female=4442;non_cancer_AN_asj_male=2289;non_cancer_AN_eas=12698;non_cancer_AN_eas_female=8760;non_cancer_AN_eas_jpn=61;non_cancer_AN_eas_kor=2828;non_cancer_AN_eas_male=3938;non_cancer_AN_eas_oea=9809;non_cancer_AN_female=102454;non_cancer_AN_fin=15290;non_cancer_AN_fin_female=10172;non_cancer_AN_fin_male=5118;non_cancer_AN_male=57461;non_cancer_AN_nfe=66733;non_cancer_AN_nfe_bgr=1695;non_cancer_AN_nfe_est=113;non_cancer_AN_nfe_female=41656;non_cancer_AN_nfe_male=25077;non_cancer_AN_nfe_nwe=26895;non_cancer_AN_nfe_onf=16187;non_cancer_AN_nfe_seu=5081;non_cancer_AN_nfe_swe=16762;non_cancer_AN_oth=3927;non_cancer_AN_oth_female=2572;non_cancer_AN_oth_male=1355;non_cancer_AN_popmax=9826;non_cancer_AN_raw=171473;non_cancer_AN_sas=18373;non_cancer_AN_sas_female=7446;non_cancer_AN_sas_male=10927;non_cancer_nhomalt=31;non_cancer_nhomalt_afr=12;non_cancer_nhomalt_afr_female=12;non_cancer_nhomalt_afr_male=0;non_cancer_nhomalt_amr=1;non_cancer_nhomalt_amr_female=1;non_cancer_nhomalt_amr_male=0;non_cancer_nhomalt_asj=6;non_cancer_nhomalt_asj_female=6;non_cancer_nhomalt_asj_male=0;non_cancer_nhomalt_eas=0;non_cancer_nhomalt_eas_female=0;non_cancer_nhomalt_eas_jpn=0;non_cancer_nhomalt_eas_kor=0;non_cancer_nhomalt_eas_male=0;non_cancer_nhomalt_eas_oea=0;non_cancer_nhomalt_female=31;non_cancer_nhomalt_fin=6;non_cancer_nhomalt_fin_female=6;non_cancer_nhomalt_fin_male=0;non_cancer_nhomalt_male=0;non_cancer_nhomalt_nfe=6;non_cancer_nhomalt_nfe_bgr=1;non_cancer_nhomalt_nfe_est=0;non_cancer_nhomalt_nfe_female=6;non_cancer_nhomalt_nfe_male=0;non_cancer_nhomalt_nfe_nwe=2;non_cancer_nhomalt_nfe_onf=1;non_cancer_nhomalt_nfe_seu=0;non_cancer_nhomalt_nfe_swe=2;non_cancer_nhomalt_oth=0;non_cancer_nhomalt_oth_female=0;non_cancer_nhomalt_oth_male=0;non_cancer_nhomalt_popmax=12;non_cancer_nhomalt_raw=47;non_cancer_nhomalt_sas=0;non_cancer_nhomalt_sas_female=0;non_cancer_nhomalt_sas_male=0;non_cancer_popmax=afr;non_neuro_AC=2054;non_neuro_AC_afr=565;non_neuro_AC_afr_female=463;non_neuro_AC_afr_male=102;non_neuro_AC_amr=136;non_neuro_AC_amr_female=114;non_neuro_AC_amr_male=22;non_neuro_AC_asj=204;non_neuro_AC_asj_female=164;non_neuro_AC_asj_male=40;non_neuro_AC_eas=10;non_neuro_AC_eas_female=9;non_neuro_AC_eas_jpn=0;non_neuro_AC_eas_kor=4;non_neuro_AC_eas_male=1;non_neuro_AC_eas_oea=6;non_neuro_AC_female=1561;non_neuro_AC_fin=302;non_neuro_AC_fin_female=206;non_neuro_AC_fin_male=96;non_neuro_AC_male=493;non_neuro_AC_nfe=728;non_neuro_AC_nfe_bgr=3;non_neuro_AC_nfe_est=1;non_neuro_AC_nfe_female=544;non_neuro_AC_nfe_male=184;non_neuro_AC_nfe_nwe=331;non_neuro_AC_nfe_onf=236;non_neuro_AC_nfe_seu=63;non_neuro_AC_nfe_swe=94;non_neuro_AC_oth=39;non_neuro_AC_oth_female=29;non_neuro_AC_oth_male=10;non_neuro_AC_popmax=565;non_neuro_AC_raw=2598;non_neuro_AC_sas=70;non_neuro_AC_sas_female=32;non_neuro_AC_sas_male=38;non_neuro_AF=1.46962e-02;non_neuro_AF_afr=5.26610e-02;non_neuro_AF_afr_female=5.58370e-02;non_neuro_AF_afr_male=4.18547e-02;non_neuro_AF_amr=5.77814e-03;non_neuro_AF_amr_female=6.33122e-03;non_neuro_AF_amr_male=3.97758e-03;non_neuro_AF_asj=4.74639e-02;non_neuro_AF_asj_female=5.64738e-02;non_neuro_AF_asj_male=2.86944e-02;non_neuro_AF_eas=1.02987e-03;non_neuro_AF_eas_female=1.35095e-03;non_neuro_AF_eas_jpn=0.00000e+00;non_neuro_AF_eas_kor=1.40252e-03;non_neuro_AF_eas_male=3.28084e-04;non_neuro_AF_eas_oea=8.85086e-04;non_neuro_AF_female=1.73433e-02;non_neuro_AF_fin=2.59763e-02;non_neuro_AF_fin_female=2.74740e-02;non_neuro_AF_fin_male=2.32558e-02;non_neuro_AF_male=9.90795e-03;non_neuro_AF_nfe=1.25405e-02;non_neuro_AF_nfe_bgr=1.03806e-02;non_neuro_AF_nfe_est=6.41026e-03;non_neuro_AF_nfe_female=1.47457e-02;non_neuro_AF_nfe_male=8.69565e-03;non_neuro_AF_nfe_nwe=1.36698e-02;non_neuro_AF_nfe_onf=1.30372e-02;non_neuro_AF_nfe_seu=1.18488e-02;non_neuro_AF_nfe_swe=9.42450e-03;non_neuro_AF_oth=1.15248e-02;non_neuro_AF_oth_female=1.28092e-02;non_neuro_AF_oth_male=8.92857e-03;non_neuro_AF_popmax=5.26610e-02;non_neuro_AF_raw=1.71986e-02;non_neuro_AF_sas=3.79857e-03;non_neuro_AF_sas_female=4.27350e-03;non_neuro_AF_sas_male=3.47349e-03;non_neuro_AN=139764;non_neuro_AN_afr=10729;non_neuro_AN_afr_female=8292;non_neuro_AN_afr_male=2437;non_neuro_AN_amr=23537;non_neuro_AN_amr_female=18006;non_neuro_AN_amr_male=5531;non_neuro_AN_asj=4298;non_neuro_AN_asj_female=2904;non_neuro_AN_asj_male=1394;non_neuro_AN_eas=9710;non_neuro_AN_eas_female=6662;non_neuro_AN_eas_jpn=79;non_neuro_AN_eas_kor=2852;non_neuro_AN_eas_male=3048;non_neuro_AN_eas_oea=6779;non_neuro_AN_female=90006;non_neuro_AN_fin=11626;non_neuro_AN_fin_female=7498;non_neuro_AN_fin_male=4128;non_neuro_AN_male=49758;non_neuro_AN_nfe=58052;non_neuro_AN_nfe_bgr=289;non_neuro_AN_nfe_est=156;non_neuro_AN_nfe_female=36892;non_neuro_AN_nfe_male=21160;non_neuro_AN_nfe_nwe=24214;non_neuro_AN_nfe_onf=18102;non_neuro_AN_nfe_seu=5317;non_neuro_AN_nfe_swe=9974;non_neuro_AN_oth=3384;non_neuro_AN_oth_female=2264;non_neuro_AN_oth_male=1120;non_neuro_AN_popmax=10729;non_neuro_AN_raw=151059;non_neuro_AN_sas=18428;non_neuro_AN_sas_female=7488;non_neuro_AN_sas_male=10940;non_neuro_faf95=1.38409e-02;non_neuro_faf95_afr=4.73059e-02;non_neuro_faf95_amr=5.67405e-03;non_neuro_faf95_eas=4.06800e-04;non_neuro_faf95_nfe=1.13728e-02;non_neuro_faf95_sas=2.25409e-03;non_neuro_faf99=1.38412e-02;non_neuro_faf99_afr=4.73059e-02;non_neuro_faf99_amr=5.67391e-03;non_neuro_faf99_eas=4.06860e-04;non_neuro_faf99_nfe=1.13729e-02;non_neuro_faf99_sas=2.25438e-03;non_neuro_nhomalt=25;non_neuro_nhomalt_afr=13;non_neuro_nhomalt_afr_female=13;non_neuro_nhomalt_afr_male=0;non_neuro_nhomalt_amr=1;non_neuro_nhomalt_amr_female=1;non_neuro_nhomalt_amr_male=0;non_neuro_nhomalt_asj=5;non_neuro_nhomalt_asj_female=5;non_neuro_nhomalt_asj_male=0;non_neuro_nhomalt_eas=0;non_neuro_nhomalt_eas_female=0;non_neuro_nhomalt_eas_jpn=0;non_neuro_nhomalt_eas_kor=0;non_neuro_nhomalt_eas_male=0;non_neuro_nhomalt_eas_oea=0;non_neuro_nhomalt_female=25;non_neuro_nhomalt_fin=4;non_neuro_nhomalt_fin_female=4;non_neuro_nhomalt_fin_male=0;non_neuro_nhomalt_male=0;non_neuro_nhomalt_nfe=2;non_neuro_nhomalt_nfe_bgr=0;non_neuro_nhomalt_nfe_est=0;non_neuro_nhomalt_nfe_female=2;non_neuro_nhomalt_nfe_male=0;non_neuro_nhomalt_nfe_nwe=1;non_neuro_nhomalt_nfe_onf=1;non_neuro_nhomalt_nfe_seu=0;non_neuro_nhomalt_nfe_swe=0;non_neuro_nhomalt_oth=0;non_neuro_nhomalt_oth_female=0;non_neuro_nhomalt_oth_male=0;non_neuro_nhomalt_popmax=13;non_neuro_nhomalt_raw=45;non_neuro_nhomalt_sas=0;non_neuro_nhomalt_sas_female=0;non_neuro_nhomalt_sas_male=0;non_neuro_popmax=afr;non_topmed_AC=2356;non_topmed_AC_afr=449;non_topmed_AC_afr_female=355;non_topmed_AC_afr_male=94;non_topmed_AC_amr=166;non_topmed_AC_amr_female=137;non_topmed_AC_amr_male=29;non_topmed_AC_asj=337;non_topmed_AC_asj_female=256;non_topmed_AC_asj_male=81;non_topmed_AC_eas=11;non_topmed_AC_eas_female=10;non_topmed_AC_eas_jpn=0;non_topmed_AC_eas_kor=4;non_topmed_AC_eas_male=1;non_topmed_AC_eas_oea=7;non_topmed_AC_female=1756;non_topmed_AC_fin=382;non_topmed_AC_fin_female=271;non_topmed_AC_fin_male=111;non_topmed_AC_male=600;non_topmed_AC_nfe=886;non_topmed_AC_nfe_bgr=28;non_topmed_AC_nfe_est=1;non_topmed_AC_nfe_female=654;non_topmed_AC_nfe_male=232;non_topmed_AC_nfe_nwe=379;non_topmed_AC_nfe_onf=264;non_topmed_AC_nfe_seu=71;non_topmed_AC_nfe_swe=143;non_topmed_AC_oth=55;non_topmed_AC_oth_female=41;non_topmed_AC_oth_male=14;non_topmed_AC_popmax=449;non_topmed_AC_raw=2955;non_topmed_AC_sas=70;non_topmed_AC_sas_female=32;non_topmed_AC_sas_male=38;non_topmed_AF=1.42543e-02;non_topmed_AF_afr=5.59781e-02;non_topmed_AF_afr_female=5.86196e-02;non_topmed_AF_afr_male=4.78372e-02;non_topmed_AF_amr=6.27552e-03;non_topmed_AF_amr_female=6.87268e-03;non_topmed_AF_amr_male=4.44922e-03;non_topmed_AF_asj=4.80125e-02;non_topmed_AF_asj_female=5.47711e-02;non_topmed_AF_asj_male=3.45416e-02;non_topmed_AF_eas=8.36057e-04;non_topmed_AF_eas_female=1.09890e-03;non_topmed_AF_eas_jpn=0.00000e+00;non_topmed_AF_eas_kor=1.40154e-03;non_topmed_AF_eas_male=2.46488e-04;non_topmed_AF_eas_oea=6.84664e-04;non_topmed_AF_female=1.65426e-02;non_topmed_AF_fin=2.49657e-02;non_topmed_AF_fin_female=2.66156e-02;non_topmed_AF_fin_male=2.16839e-02;non_topmed_AF_male=1.01466e-02;non_topmed_AF_nfe=1.21866e-02;non_topmed_AF_nfe_bgr=1.57392e-02;non_topmed_AF_nfe_est=5.84795e-03;non_topmed_AF_nfe_female=1.42291e-02;non_topmed_AF_nfe_male=8.67582e-03;non_topmed_AF_nfe_nwe=1.34909e-02;non_topmed_AF_nfe_onf=1.33509e-02;non_topmed_AF_nfe_seu=1.26245e-02;non_topmed_AF_nfe_swe=8.28409e-03;non_topmed_AF_oth=1.31046e-02;non_topmed_AF_oth_female=1.48983e-02;non_topmed_AF_oth_male=9.68858e-03;non_topmed_AF_popmax=5.59781e-02;non_topmed_AF_raw=1.66616e-02;non_topmed_AF_sas=3.79754e-03;non_topmed_AF_sas_female=4.27236e-03;non_topmed_AF_sas_male=3.47254e-03;non_topmed_AN=165283;non_topmed_AN_afr=8021;non_topmed_AN_afr_female=6056;non_topmed_AN_afr_male=1965;non_topmed_AN_amr=26452;non_topmed_AN_amr_female=19934;non_topmed_AN_amr_male=6518;non_topmed_AN_asj=7019;non_topmed_AN_asj_female=4674;non_topmed_AN_asj_male=2345;non_topmed_AN_eas=13157;non_topmed_AN_eas_female=9100;non_topmed_AN_eas_jpn=79;non_topmed_AN_eas_kor=2854;non_topmed_AN_eas_male=4057;non_topmed_AN_eas_oea=10224;non_topmed_AN_female=106150;non_topmed_AN_fin=15301;non_topmed_AN_fin_female=10182;non_topmed_AN_fin_male=5119;non_topmed_AN_male=59133;non_topmed_AN_nfe=72703;non_topmed_AN_nfe_bgr=1779;non_topmed_AN_nfe_est=171;non_topmed_AN_nfe_female=45962;non_topmed_AN_nfe_male=26741;non_topmed_AN_nfe_nwe=28093;non_topmed_AN_nfe_onf=19774;non_topmed_AN_nfe_seu=5624;non_topmed_AN_nfe_swe=17262;non_topmed_AN_oth=4197;non_topmed_AN_oth_female=2752;non_topmed_AN_oth_male=1445;non_topmed_AN_popmax=8021;non_topmed_AN_raw=177354;non_topmed_AN_sas=18433;non_topmed_AN_sas_female=7490;non_topmed_AN_sas_male=10943;non_topmed_nhomalt=30;non_topmed_nhomalt_afr=11;non_topmed_nhomalt_afr_female=11;non_topmed_nhomalt_afr_male=0;non_topmed_nhomalt_amr=1;non_topmed_nhomalt_amr_female=1;non_topmed_nhomalt_amr_male=0;non_topmed_nhomalt_asj=6;non_topmed_nhomalt_asj_female=6;non_topmed_nhomalt_asj_male=0;non_topmed_nhomalt_eas=0;non_topmed_nhomalt_eas_female=0;non_topmed_nhomalt_eas_jpn=0;non_topmed_nhomalt_eas_kor=0;non_topmed_nhomalt_eas_male=0;non_topmed_nhomalt_eas_oea=0;non_topmed_nhomalt_female=30;non_topmed_nhomalt_fin=6;non_topmed_nhomalt_fin_female=6;non_topmed_nhomalt_fin_male=0;non_topmed_nhomalt_male=0;non_topmed_nhomalt_nfe=6;non_topmed_nhomalt_nfe_bgr=1;non_topmed_nhomalt_nfe_est=0;non_topmed_nhomalt_nfe_female=6;non_topmed_nhomalt_nfe_male=0;non_topmed_nhomalt_nfe_nwe=2;non_topmed_nhomalt_nfe_onf=1;non_topmed_nhomalt_nfe_seu=0;non_topmed_nhomalt_nfe_swe=2;non_topmed_nhomalt_oth=0;non_topmed_nhomalt_oth_female=0;non_topmed_nhomalt_oth_male=0;non_topmed_nhomalt_popmax=11;non_topmed_nhomalt_raw=49;non_topmed_nhomalt_sas=0;non_topmed_nhomalt_sas_female=0;non_topmed_nhomalt_sas_male=0;non_topmed_popmax=afr;nonpar;pab_max=1.00000e+00;popmax=afr;rf_tp_probability=7.84117e-01;segdup;variant_type=mixed;vep=AGCCGG|inframe_insertion|MODERATE|ZRSR2|ENSG00000169249|Transcript|ENST00000307771|protein_coding|11/11||ENST00000307771.7:c.1338_1343dupGAGCCG|ENSP00000303015.7:p.Ser447_Arg448dup|1338-1339|1314-1315|438-439|-/SR|-/AGCCGG|rs752736259|1||1||insertion|1|HGNC|23019|YES|||CCDS14172.1|ENSP00000303015|Q15696||UPI0000137929||||Low_complexity_(Seg):seg&hmmpanther:PTHR12620:SF6&hmmpanther:PTHR12620|29|AGCCGG:0.0236||AGCCGG:0.0492|AGCCGG:0.0086|AGCCGG:0|AGCCGG:0.0159|AGCCGG:0.002||||||||||||||||||||||,AGCCGG|downstream_gene_variant|MODIFIER|AP1S2|ENSG00000182287|Transcript|ENST00000329235|protein_coding||||||||||rs752736259|1|2698|-1||insertion|1|HGNC|560|YES|||CCDS14173.1|ENSP00000328789|P56377|Q549M9|UPI0000124FEC|1|||||AGCCGG:0.0236||AGCCGG:0.0492|AGCCGG:0.0086|AGCCGG:0|AGCCGG:0.0159|AGCCGG:0.002||||||||||||||||||||||,AGCCGG|downstream_gene_variant|MODIFIER|AP1S2|ENSG00000182287|Transcript|ENST00000452376|protein_coding||||||||||rs752736259|1|3784|-1|cds_start_NF|insertion|1|HGNC|560|||||ENSP00000403498|||UPI000059DAD2|1|||||AGCCGG:0.0236||AGCCGG:0.0492|AGCCGG:0.0086|AGCCGG:0|AGCCGG:0.0159|AGCCGG:0.002||||||||||||||||||||||;was_mixed

I have run this variant using the cache but the same output was observed where this variant was not annotated. The gnomad r2.1.1 was used. The command was:

docker run -v /home/dnanexus:/opt/vep/.vep ensemblorg/ensembl-vep:release_103.1 ./vep -i /opt/vep/.vep/130_split.vcf -o /opt/vep/.vep/130_split_filevep.vcf --vcf --cache --refseq --exclude_predicted --symbol --hgvs --af_gnomad --check_existing --variant_class --numbers --offline --custom /opt/vep/.vep/clinvar_20240611_GRCh38.vcf.gz,ClinVar,vcf,exact,0,CLNSIG,CLNREVSTAT,CLNDN --custom /opt/vep/.vep/h_samples_withoutchr.vcf.gz,Prev,vcf,exact,0,AC,NS --custom /opt/vep/.vep/CosmicCodingMuts_GRCh38_v99.normal.vcf.gz,COSMIC,vcf,exact,0,ID --custom /opt/vep/.vep/CosmicNonCodingVariants_GRCh38_v99.normal.vcf.gz,COSMIC,vcf,exact,0,ID --plugin CADD,/opt/vep/.vep/./whole_genome_SNVs.tsv.gz,/opt/vep/.vep/./gnomad.genomes.r3.0.indel.tsv.gz --fields SYMBOL,VARIANT_CLASS,Consequence,EXON,HGVSc,HGVSp,gnomAD_AF,CADD_PHRED,Existing_variation,ClinVar,ClinVar_CLNDN,ClinVar_CLNSIG,COSMIC,Prev_AC,Prev_NS,Feature --fork 4 --no_stats

I also tested using the online VEP to see if this would not be annotated by VEP but found that the variant was annotated correctly, I have attached the output of this VEP job:
vep_online.txt

I am aware that the online is a more recent version of vep 112 but I want to understand what caused this variant to not be annotated by gnomADe correctly.

System

• VEP version: 103
• VEP Cache version: 103
• Perl version: N/A
• OS: Ubuntu 20.04
• tabix installed: Yes

[dglemos]

Hi @Aisha-D,
Can you please run vep with the minimal options, something like this:

docker run -v /home/dnanexus:/opt/vep/.vep ensemblorg/ensembl-vep:release_103.1 ./vep \
-i /opt/vep/.vep/variant.vcf \
-o /opt/vep/.vep/output.txt \
--offline \
--cache_version 103 \
--refseq \
--af_gnomad

variant.vcf containing only:
chrX 15823107 . C CAGCCGG . . .

[Aisha-D]

Hi,

I have run this locally and it does not produce any gnomAD annotations. Below is my command:

sudo docker run  -v /home/dnanexus:/opt/vep/.vep ensemblorg/ensembl-vep:release_103.1  ./vep -i /opt/vep/.vep/variant.vcf -o /opt/vep/.vep/out.vcf --offline --cache_version 103 --refseq --af_gnomad --use_given_ref --force

The results:

$ grep -v ^"#" out.vcf
X_15823108_-/AGCCGG     X:15823107-15823108     AGCCGG  8905    NM_001272071.2  Transcript      downstream_gene_variant -       -       -       -       -       -       IMPACT=MODIFIER;DISTANCE=2698;STRAND=-1
X_15823108_-/AGCCGG     X:15823107-15823108     AGCCGG  8905    NM_003916.5     Transcript      downstream_gene_variant -       -       -       -       -       -       IMPACT=MODIFIER;DISTANCE=2698;STRAND=-1
X_15823108_-/AGCCGG     X:15823107-15823108     AGCCGG  8233    NM_005089.4     Transcript      inframe_insertion       1326-1327       1314-1315       438-439 -/SR    -/AGCCGG        -       IMPACT=MODERATE;STRAND=1
X_15823108_-/AGCCGG     X:15823107-15823108     AGCCGG  8233    XM_005274597.3  Transcript      inframe_insertion       1327-1328       900-901 300-301 -/SR    -/AGCCGG        -       IMPACT=MODERATE;STRAND=1
X_15823108_-/AGCCGG     X:15823107-15823108     AGCCGG  8233    XM_011545589.3  Transcript      inframe_insertion       1291-1292       1236-1237       412-413 -/SR    -/AGCCGG        -       IMPACT=MODERATE;STRAND=1
X_15823108_-/AGCCGG     X:15823107-15823108     AGCCGG  8233    XM_017029881.2  Transcript      inframe_insertion       1326-1327       1314-1315       438-439 -/SR    -/AGCCGG        -       IMPACT=MODERATE;STRAND=1
X_15823108_-/AGCCGG     X:15823107-15823108     AGCCGG  8233    XM_017029882.2  Transcript      inframe_insertion       1281-1282       900-901 300-301 -/SR    -/AGCCGG        -       IMPACT=MODERATE;STRAND=1
X_15823108_-/AGCCGG     X:15823107-15823108     AGCCGG  8233    XM_017029883.2  Transcript      inframe_insertion       1422-1423       900-901 300-301 -/SR    -/AGCCGG        -       IMPACT=MODERATE;STRAND=1
X_15823108_-/AGCCGG     X:15823107-15823108     AGCCGG  8233    XM_024452455.1  Transcript      inframe_insertion       1450-1451       900-901 300-301 -/SR    -/AGCCGG        -       IMPACT=MODERATE;STRAND=1
X_15823108_-/AGCCGG     X:15823107-15823108     AGCCGG  8233    XM_024452456.1  Transcript      inframe_insertion       1475-1476       900-901 300-301 -/SR    -/AGCCGG        -       IMPACT=MODERATE;STRAND=1
X_15823108_-/AGCCGG     X:15823107-15823108     AGCCGG  8905    XR_002958809.1  Transcript      downstream_gene_variant -       -       -       -       -       -       IMPACT=MODIFIER;DISTANCE=2700;STRAND=-1
X_15823108_-/AGCCGG     X:15823107-15823108     AGCCGG  8905    XR_247289.3     Transcript      downstream_gene_variant -       -       -       -       -       -       IMPACT=MODIFIER;DISTANCE=2700;STRAND=-1

There was no gnomad annotation to this variant.