Hello,
I see some variants labeled as variant_type=multi-snv and n_alt_alleles=2, but with no other variants or alt alleles at that position in the VCF (example below, I am using gnomAD v4.0).
What does this multi-SNV classification mean for these variants?
chr22 20394630 . T C . PASS AC=1;AN=833036;AF=1.20043e-06;grpmax=sas;AC_XX=0;AF_XX=0;AN_XX=448350;nhomalt_XX=0;AC_XY=1;AF_XY=2.59952e-06;AN_XY=384686;nhomalt_XY=0;nhomalt=0;AC_afr_XX=0;AF_afr_XX=0;AN_afr_XX=9040;nhomalt_afr_XX=0;AC_afr_XY=0;AF_afr_XY=0;AN_afr_XY=6746;nhomalt_afr_XY=0;AC_afr=0;AF_afr=0;AN_afr=15786;nhomalt_afr=0;AC_amr_XX=0;AF_amr_XX=0;AN_amr_XX=650;nhomalt_amr_XX=0;AC_amr_XY=0;AF_amr_XY=0;AN_amr_XY=334;nhomalt_amr_XY=0;AC_amr=0;AF_amr=0;AN_amr=984;nhomalt_amr=0;AC_asj_XX=0;AF_asj_XX=0;AN_asj_XX=2798;nhomalt_asj_XX=0;AC_asj_XY=0;AF_asj_XY=0;AN_asj_XY=2354;nhomalt_asj_XY=0;AC_asj=0;AF_asj=0;AN_asj=5152;nhomalt_asj=0;AC_eas_XX=0;AF_eas_XX=0;AN_eas_XX=2414;nhomalt_eas_XX=0;AC_eas_XY=0;AF_eas_XY=0;AN_eas_XY=1216;nhomalt_eas_XY=0;AC_eas=0;AF_eas=0;AN_eas=3630;nhomalt_eas=0;AC_fin_XX=0;AF_fin_XX=0;AN_fin_XX=250;nhomalt_fin_XX=0;AC_fin_XY=0;AF_fin_XY=0;AN_fin_XY=26;nhomalt_fin_XY=0;AC_fin=0;AF_fin=0;AN_fin=276;nhomalt_fin=0;AC_mid_XX=0;AF_mid_XX=0;AN_mid_XX=590;nhomalt_mid_XX=0;AC_mid_XY=0;AF_mid_XY=0;AN_mid_XY=1028;nhomalt_mid_XY=0;AC_mid=0;AF_mid=0;AN_mid=1618;nhomalt_mid=0;AC_nfe_XX=0;AF_nfe_XX=0;AN_nfe_XX=410022;nhomalt_nfe_XX=0;AC_nfe_XY=0;AF_nfe_XY=0;AN_nfe_XY=351812;nhomalt_nfe_XY=0;AC_nfe=0;AF_nfe=0;AN_nfe=761834;nhomalt_nfe=0;AC_non_ukb_XX=0;AN_non_ukb_XX=0;nhomalt_non_ukb_XX=0;AC_non_ukb_XY=0;AN_non_ukb_XY=0;nhomalt_non_ukb_XY=0;AC_non_ukb=0;AN_non_ukb=0;nhomalt_non_ukb=0;AC_non_ukb_afr_XX=0;AN_non_ukb_afr_XX=0;nhomalt_non_ukb_afr_XX=0;AC_non_ukb_afr_XY=0;AN_non_ukb_afr_XY=0;nhomalt_non_ukb_afr_XY=0;AC_non_ukb_afr=0;AN_non_ukb_afr=0;nhomalt_non_ukb_afr=0;AC_non_ukb_amr_XX=0;AN_non_ukb_amr_XX=0;nhomalt_non_ukb_amr_XX=0;AC_non_ukb_amr_XY=0;AN_non_ukb_amr_XY=0;nhomalt_non_ukb_amr_XY=0;AC_non_ukb_amr=0;AN_non_ukb_amr=0;nhomalt_non_ukb_amr=0;AC_non_ukb_asj_XX=0;AN_non_ukb_asj_XX=0;nhomalt_non_ukb_asj_XX=0;AC_non_ukb_asj_XY=0;AN_non_ukb_asj_XY=0;nhomalt_non_ukb_asj_XY=0;AC_non_ukb_asj=0;AN_non_ukb_asj=0;nhomalt_non_ukb_asj=0;AC_non_ukb_eas_XX=0;AN_non_ukb_eas_XX=0;nhomalt_non_ukb_eas_XX=0;AC_non_ukb_eas_XY=0;AN_non_ukb_eas_XY=0;nhomalt_non_ukb_eas_XY=0;AC_non_ukb_eas=0;AN_non_ukb_eas=0;nhomalt_non_ukb_eas=0;AC_non_ukb_fin_XX=0;AN_non_ukb_fin_XX=0;nhomalt_non_ukb_fin_XX=0;AC_non_ukb_fin_XY=0;AN_non_ukb_fin_XY=0;nhomalt_non_ukb_fin_XY=0;AC_non_ukb_fin=0;AN_non_ukb_fin=0;nhomalt_non_ukb_fin=0;AC_non_ukb_mid_XX=0;AN_non_ukb_mid_XX=0;nhomalt_non_ukb_mid_XX=0;AC_non_ukb_mid_XY=0;AN_non_ukb_mid_XY=0;nhomalt_non_ukb_mid_XY=0;AC_non_ukb_mid=0;AN_non_ukb_mid=0;nhomalt_non_ukb_mid=0;AC_non_ukb_nfe_XX=0;AN_non_ukb_nfe_XX=0;nhomalt_non_ukb_nfe_XX=0;AC_non_ukb_nfe_XY=0;AN_non_ukb_nfe_XY=0;nhomalt_non_ukb_nfe_XY=0;AC_non_ukb_nfe=0;AN_non_ukb_nfe=0;nhomalt_non_ukb_nfe=0;AC_non_ukb_raw=0;AN_non_ukb_raw=0;nhomalt_non_ukb_raw=0;AC_non_ukb_remaining_XX=0;AN_non_ukb_remaining_XX=0;nhomalt_non_ukb_remaining_XX=0;AC_non_ukb_remaining_XY=0;AN_non_ukb_remaining_XY=0;nhomalt_non_ukb_remaining_XY=0;AC_non_ukb_remaining=0;AN_non_ukb_remaining=0;nhomalt_non_ukb_remaining=0;AC_non_ukb_sas_XX=0;AN_non_ukb_sas_XX=0;nhomalt_non_ukb_sas_XX=0;AC_non_ukb_sas_XY=0;AN_non_ukb_sas_XY=0;nhomalt_non_ukb_sas_XY=0;AC_non_ukb_sas=0;AN_non_ukb_sas=0;nhomalt_non_ukb_sas=0;AC_raw=1;AF_raw=1.20034e-06;AN_raw=833098;nhomalt_raw=0;AC_remaining_XX=0;AF_remaining_XX=0;AN_remaining_XX=15048;nhomalt_remaining_XX=0;AC_remaining_XY=0;AF_remaining_XY=0;AN_remaining_XY=12250;nhomalt_remaining_XY=0;AC_remaining=0;AF_remaining=0;AN_remaining=27298;nhomalt_remaining=0;AC_sas_XX=0;AF_sas_XX=0;AN_sas_XX=7538;nhomalt_sas_XX=0;AC_sas_XY=1;AF_sas_XY=0.000112108;AN_sas_XY=8920;nhomalt_sas_XY=0;AC_sas=1;AF_sas=6.07607e-05;AN_sas=16458;nhomalt_sas=0;AC_joint_XX=0;AF_joint_XX=0;AN_joint_XX=448350;nhomalt_joint_XX=0;AC_joint_XY=1;AF_joint_XY=2.59952e-06;AN_joint_XY=384686;nhomalt_joint_XY=0;AC_joint=1;AF_joint=1.20043e-06;AN_joint=833036;nhomalt_joint=0;AC_joint_afr_XX=0;AF_joint_afr_XX=0;AN_joint_afr_XX=9040;nhomalt_joint_afr_XX=0;AC_joint_afr_XY=0;AF_joint_afr_XY=0;AN_joint_afr_XY=6746;nhomalt_joint_afr_XY=0;AC_joint_afr=0;AF_joint_afr=0;AN_joint_afr=15786;nhomalt_joint_afr=0;AC_joint_ami_XX=0;AN_joint_ami_XX=0;nhomalt_joint_ami_XX=0;AC_joint_ami_XY=0;AN_joint_ami_XY=0;nhomalt_joint_ami_XY=0;AC_joint_ami=0;AN_joint_ami=0;nhomalt_joint_ami=0;AC_joint_amr_XX=0;AF_joint_amr_XX=0;AN_joint_amr_XX=650;nhomalt_joint_amr_XX=0;AC_joint_amr_XY=0;AF_joint_amr_XY=0;AN_joint_amr_XY=334;nhomalt_joint_amr_XY=0;AC_joint_amr=0;AF_joint_amr=0;AN_joint_amr=984;nhomalt_joint_amr=0;AC_joint_asj_XX=0;AF_joint_asj_XX=0;AN_joint_asj_XX=2798;nhomalt_joint_asj_XX=0;AC_joint_asj_XY=0;AF_joint_asj_XY=0;AN_joint_asj_XY=2354;nhomalt_joint_asj_XY=0;AC_joint_asj=0;AF_joint_asj=0;AN_joint_asj=5152;nhomalt_joint_asj=0;AC_joint_eas_XX=0;AF_joint_eas_XX=0;AN_joint_eas_XX=2414;nhomalt_joint_eas_XX=0;AC_joint_eas_XY=0;AF_joint_eas_XY=0;AN_joint_eas_XY=1216;nhomalt_joint_eas_XY=0;AC_joint_eas=0;AF_joint_eas=0;AN_joint_eas=3630;nhomalt_joint_eas=0;AC_joint_fin_XX=0;AF_joint_fin_XX=0;AN_joint_fin_XX=250;nhomalt_joint_fin_XX=0;AC_joint_fin_XY=0;AF_joint_fin_XY=0;AN_joint_fin_XY=26;nhomalt_joint_fin_XY=0;AC_joint_fin=0;AF_joint_fin=0;AN_joint_fin=276;nhomalt_joint_fin=0;AC_joint_mid_XX=0;AF_joint_mid_XX=0;AN_joint_mid_XX=590;nhomalt_joint_mid_XX=0;AC_joint_mid_XY=0;AF_joint_mid_XY=0;AN_joint_mid_XY=1028;nhomalt_joint_mid_XY=0;AC_joint_mid=0;AF_joint_mid=0;AN_joint_mid=1618;nhomalt_joint_mid=0;AC_joint_nfe_XX=0;AF_joint_nfe_XX=0;AN_joint_nfe_XX=410022;nhomalt_joint_nfe_XX=0;AC_joint_nfe_XY=0;AF_joint_nfe_XY=0;AN_joint_nfe_XY=351812;nhomalt_joint_nfe_XY=0;AC_joint_nfe=0;AF_joint_nfe=0;AN_joint_nfe=761834;nhomalt_joint_nfe=0;AC_joint_raw=1;AF_joint_raw=1.20034e-06;AN_joint_raw=833098;nhomalt_joint_raw=0;AC_joint_remaining_XX=0;AF_joint_remaining_XX=0;AN_joint_remaining_XX=15048;nhomalt_joint_remaining_XX=0;AC_joint_remaining_XY=0;AF_joint_remaining_XY=0;AN_joint_remaining_XY=12250;nhomalt_joint_remaining_XY=0;AC_joint_remaining=0;AF_joint_remaining=0;AN_joint_remaining=27298;nhomalt_joint_remaining=0;AC_joint_sas_XX=0;AF_joint_sas_XX=0;AN_joint_sas_XX=7538;nhomalt_joint_sas_XX=0;AC_joint_sas_XY=1;AF_joint_sas_XY=0.000112108;AN_joint_sas_XY=8920;nhomalt_joint_sas_XY=0;AC_joint_sas=1;AF_joint_sas=6.07607e-05;AN_joint_sas=16458;nhomalt_joint_sas=0;AC_grpmax=1;AF_grpmax=6.07607e-05;AN_grpmax=16458;nhomalt_grpmax=0;nhomalt_grpmax_non_ukb=2147483647;grpmax_joint=sas;AC_grpmax_joint=1;AF_grpmax_joint=6.07607e-05;AN_grpmax_joint=16458;nhomalt_grpmax_joint=0;faf95=0;faf95_afr=0;faf95_amr=0;faf95_eas=0;faf95_nfe=0;faf95_non_ukb=0;faf95_non_ukb_afr=0;faf95_non_ukb_amr=0;faf95_non_ukb_eas=0;faf95_non_ukb_nfe=0;faf95_non_ukb_sas=0;faf95_sas=0;faf99=0;faf99_afr=0;faf99_amr=0;faf99_eas=0;faf99_nfe=0;faf99_non_ukb=0;faf99_non_ukb_afr=0;faf99_non_ukb_amr=0;faf99_non_ukb_eas=0;faf99_non_ukb_nfe=0;faf99_non_ukb_sas=0;faf99_sas=0;faf95_joint=0;faf95_joint_afr=0;faf95_joint_amr=0;faf95_joint_eas=0;faf95_joint_nfe=0;faf95_joint_sas=0;faf99_joint=0;faf99_joint_afr=0;faf99_joint_amr=0;faf99_joint_eas=0;faf99_joint_nfe=0;faf99_joint_sas=0;age_hist_het_bin_freq=0|0|0|1|0|0|0|0|0|0;age_hist_het_n_smaller=0;age_hist_het_n_larger=0;age_hist_hom_bin_freq=0|0|0|0|0|0|0|0|0|0;age_hist_hom_n_smaller=0;age_hist_hom_n_larger=0;FS=9.19374;MQ=60;MQRankSum=0;QUALapprox=523;QD=7.57971;ReadPosRankSum=0.701;SOR=1.91102;VarDP=69;AS_FS=3.87322;AS_MQ=60;AS_MQRankSum=0;AS_pab_max=0.48685;AS_QUALapprox=501;AS_QD=15.1818;AS_ReadPosRankSum=0.511;AS_SB_TABLE=24,19|13,6;AS_SOR=1.26976;AS_VarDP=33;inbreeding_coeff=-1.20034e-06;AS_culprit=AS_MQ;AS_VQSLOD=5.6593;allele_type=snv;n_alt_alleles=2;variant_type=multi-snv;fail_interval_qc;gq_hist_alt_bin_freq=0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|1;gq_hist_all_bin_freq=0|0|0|0|58|0|259|0|842|0|2253|0|413105|0|0|0|0|0|0|1;dp_hist_alt_bin_freq=0|0|0|0|0|0|1|0|0|0|0|0|0|0|0|0|0|0|0|0;dp_hist_alt_n_larger=0;dp_hist_all_bin_freq=0|0|55|700|2686|74083|297703|39638|1514|112|15|8|2|1|1|0|0|0|0|0;dp_hist_all_n_larger=0;ab_hist_alt_bin_freq=0|0|0|0|0|0|0|0|0|0|0|1|0|0|0|0|0|0|0|0;cadd_raw_score=3.41568;cadd_phred=24.4;revel_max=0.336;spliceai_ds_max=0;pangolin_largest_ds=-0.01;phylop=4.283;sift_max=0;polyphen_max=0.95;VRS_Allele_IDs=ga4gh:VA.FF6sqhDqhF1fBDBtWWSn-MQL3rOkMtj_,ga4gh:VA.chFhCgjVZpmP39oQbMZBJGf865laZfxe;VRS_Starts=20394629,20394629;VRS_Ends=20394630,20394630;VRS_States=T,C;vep=C|intron_variant|MODIFIER|ZNF74|ENSG00000185252|Transcript|ENST00000357502|protein_coding||1/4|ENST00000357502.5:c.50+296T>C|||||||1||1||SNV|HGNC|HGNC:13144||||1|||ENSP00000350101||Ensembl|||||||||||||||,C|start_lost|HIGH|ZNF74|ENSG00000185252|Transcript|ENST00000400451|protein_coding|1/5||ENST00000400451.7:c.2T>C|ENSP00000383301.2:p.Met1?|480|2|1|M/T|aTg/aCg|1||1||SNV|HGNC|HGNC:13144|YES|NM_003426.4||1|P2|CCDS42982.1|ENSP00000383301|Q16587-1|Ensembl|||||||||||||||,C|start_lost|HIGH|ZNF74|ENSG00000185252|Transcript|ENST00000403682|protein_coding|1/4||ENST00000403682.7:c.2T>C|ENSP00000384750.3:p.Met1?|503|2|1|M/T|aTg/aCg|1||1||SNV|HGNC|HGNC:13144||||1||CCDS58794.1|ENSP00000384750|Q16587-5|Ensembl|||||||||||||||,C|start_lost|HIGH|ZNF74|ENSG00000185252|Transcript|ENST00000405993|protein_coding|1/4||ENST00000405993.2:c.2T>C|ENSP00000385855.1:p.Met1?|2|2|1|M/T|aTg/aCg|1||1||SNV|HGNC|HGNC:13144||||5|A2||ENSP00000385855|Q16587-3|Ensembl|||||||||||||||,C|start_lost|HIGH|ZNF74|ENSG00000185252|Transcript|ENST00000420626|protein_coding|1/2||ENST00000420626.1:c.2T>C|ENSP00000397011.1:p.Met1?|442|2|1|M/T|aTg/aCg|1||1||SNV|HGNC|HGNC:13144||||4|||ENSP00000397011||Ensembl|||||||||||||||,C|start_lost&NMD_transcript_variant|HIGH|ZNF74|ENSG00000185252|Transcript|ENST00000437275|nonsense_mediated_decay|1/6||ENST00000437275.5:c.2T>C|ENSP00000395437.1:p.Met1?|228|2|1|M/T|aTg/aCg|1||1||SNV|HGNC|HGNC:13144||||1|||ENSP00000395437||Ensembl|||||||||||||||,C|upstream_gene_variant|MODIFIER|ZNF74|ENSG00000185252|Transcript|ENST00000476678|retained_intron||||||||||1|4881|1||SNV|HGNC|HGNC:13144||||2|||||Ensembl|||||||||||||||,C|non_coding_transcript_exon_variant|MODIFIER|ZNF74|ENSG00000185252|Transcript|ENST00000493734|retained_intron|1/4||ENST00000493734.5:n.443T>C||443|||||1||1||SNV|HGNC|HGNC:13144||||2|||||Ensembl|||||||||||||||,C|start_lost|HIGH|ZNF74|ENSG00000185252|Transcript|ENST00000611540|protein_coding|2/6||ENST00000611540.4:c.2T>C|ENSP00000483077.1:p.Met1?|288|2|1|M/T|aTg/aCg|1||1||SNV|HGNC|HGNC:13144||||2|P2|CCDS42982.1|ENSP00000483077|Q16587-1|Ensembl|||||||||||||||,C|start_lost|HIGH|ZNF74|7625|Transcript|NM_001256523.2|protein_coding|1/4||NM_001256523.2:c.2T>C|NP_001243452.1:p.Met1?|480|2|1|M/T|aTg/aCg|1||1||SNV|EntrezGene|HGNC:13144|||||||NP_001243452.1||RefSeq|||||||||||||||,C|start_lost|HIGH|ZNF74|7625|Transcript|NM_001256524.2|protein_coding|2/6||NM_001256524.2:c.2T>C|NP_001243453.1:p.Met1?|252|2|1|M/T|aTg/aCg|1||1||SNV|EntrezGene|HGNC:13144|||||||NP_001243453.1||RefSeq|||||||||||||||,C|intron_variant|MODIFIER|ZNF74|7625|Transcript|NM_001256525.2|protein_coding||1/4|NM_001256525.2:c.-180+296T>C|||||||1||1||SNV|EntrezGene|HGNC:13144|||||||NP_001243454.1||RefSeq|||||||||||||||,C|start_lost|HIGH|ZNF74|7625|Transcript|NM_003426.4|protein_coding|1/5||NM_003426.4:c.2T>C|NP_003417.2:p.Met1?|480|2|1|M/T|aTg/aCg|1||1||SNV|EntrezGene|HGNC:13144|YES|ENST00000400451.7|||||NP_003417.2||RefSeq|||||||||||||||,C|non_coding_transcript_exon_variant|MODIFIER|ZNF74|7625|Transcript|NR_046282.2|misc_RNA|1/6||NR_046282.2:n.480T>C||480|||||1||1||SNV|EntrezGene|HGNC:13144|||||||||RefSeq|||||||||||||||,C|upstream_gene_variant|MODIFIER|USP41|373856|Transcript|XM_017029164.1|protein_coding||||||||||1|3872|-1||SNV|EntrezGene||YES||||||XP_016884653.1||RefSeq|||||||||||||||,C|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000143891|promoter||||||||||1||||SNV||||||||||||||||||||||||||
Thank you so much!