# Multiple ref alleles at same location
**URL:** https://discuss.gnomad.broadinstitute.org/t/multiple-ref-alleles-at-same-location/583
**Category:** Multinucleotide variants
**Created:** [February 24, 2025, 2:33pm UTC](https://discuss.gnomad.broadinstitute.org/t/multiple-ref-alleles-at-same-location/583 "2025-02-24T14:33:03Z")
**Posts on this page:** 2
**Page:** 1
### Author:  [@Shriya\_Rangaswamy](https://discuss.gnomad.broadinstitute.org/u/Shriya_Rangaswamy)
#### Post date: [February 24, 2025, 2:33pm UTC](https://discuss.gnomad.broadinstitute.org/t/multiple-ref-alleles-at-same-location/583/1 "2025-02-24T14:33:03Z")
Not exactly an MNV question, but I was wondering why for the same chromosome and start and end positions, gnomAD v4.1.0 sometimes lists multiple ref alleles. For example, when I use pytabix to query the chr 22 joint exomes and genomes vcf file for variants at position 10522592, I see that both A and G are possible ref alleles. I understand that a given locus can have multiple ALT alleles, but is the listing of multiple ref alleles due to the representation of alternate haplotype loci in GRCh38? Thank you so much!
---
### Author:  [@kchao](https://discuss.gnomad.broadinstitute.org/u/kchao)
#### Post date: [February 24, 2025, 10:04pm UTC](https://discuss.gnomad.broadinstitute.org/t/multiple-ref-alleles-at-same-location/583/2 "2025-02-24T22:04:39Z")
Thanks for reaching out. I checked the chr22 joint VCF and did not see multiple reference alleles; the only reference allele listed in that file is G. For example, here is one of the records in that file:
```auto
#CHROM POS ID REF ALT QUAL FILTER INFO
chr22 10522592 . G T . GENOMES_FILTERED AC_joint=0;AN_joint=100756;AF_joint=0.00000;AC_genomes=0;AN_genomes=100756;AF_genomes=0.00000;genomes_filters=AC0,AS_VQSR;AC_joint_XX=0;AF_joint_XX=0.00000;AN_joint_XX=52314;nhomalt_joint_XX=0;AC_joint_XY=0;AF_joint_XY=0.00000;AN_joint_XY=48442;nhomalt_joint_XY=0;nhomalt_joint=0;AC_joint_afr_XX=0;AF_joint_afr_XX=0.00000;AN_joint_afr_XX=16804;nhomalt_joint_afr_XX=0;AC_joint_afr_XY=0;AF_joint_afr_XY=0.00000;AN_joint_afr_XY=14556;nhomalt_joint_afr_XY=0;AC_joint_afr=0;AF_joint_afr=0.00000;AN_joint_afr=31360;nhomalt_joint_afr=0;AC_joint_ami_XX=0;AF_joint_ami_XX=0.00000;AN_joint_ami_XX=274;nhomalt_joint_ami_XX=0;AC_joint_ami_XY=0;AF_joint_ami_XY=0.00000;AN_joint_ami_XY=294;nhomalt_joint_ami_XY=0;AC_joint_ami=0;AF_joint_ami=0.00000;AN_joint_ami=568;nhomalt_joint_ami=0;AC_joint_amr_XX=0;AF_joint_amr_XX=0.00000;AN_joint_amr_XX=4074;nhomalt_joint_amr_XX=0;AC_joint_amr_XY=0;AF_joint_amr_XY=0.00000;AN_joint_amr_XY=4908;nhomalt_joint_amr_XY=0;AC_joint_amr=0;AF_joint_amr=0.00000;AN_joint_amr=8982;nhomalt_joint_amr=0;AC_joint_asj_XX=0;AF_joint_asj_XX=0.00000;AN_joint_asj_XX=1228;nhomalt_joint_asj_XX=0;AC_joint_asj_XY=0;AF_joint_asj_XY=0.00000;AN_joint_asj_XY=1078;nhomalt_joint_asj_XY=0;AC_joint_asj=0;AF_joint_asj=0.00000;AN_joint_asj=2306;nhomalt_joint_asj=0;AC_joint_eas_XX=0;AF_joint_eas_XX=0.00000;AN_joint_eas_XX=1850;nhomalt_joint_eas_XX=0;AC_joint_eas_XY=0;AF_joint_eas_XY=0.00000;AN_joint_eas_XY=2256;nhomalt_joint_eas_XY=0;AC_joint_eas=0;AF_joint_eas=0.00000;AN_joint_eas=4106;nhomalt_joint_eas=0;AC_joint_fin_XX=0;AF_joint_fin_XX=0.00000;AN_joint_fin_XX=1292;nhomalt_joint_fin_XX=0;AC_joint_fin_XY=0;AF_joint_fin_XY=0.00000;AN_joint_fin_XY=4124;nhomalt_joint_fin_XY=0;AC_joint_fin=0;AF_joint_fin=0.00000;AN_joint_fin=5416;nhomalt_joint_fin=0;AC_joint_mid_XX=0;AF_joint_mid_XX=0.00000;AN_joint_mid_XX=96;nhomalt_joint_mid_XX=0;AC_joint_mid_XY=0;AF_joint_mid_XY=0.00000;AN_joint_mid_XY=98;nhomalt_joint_mid_XY=0;AC_joint_mid=0;AF_joint_mid=0.00000;AN_joint_mid=194;nhomalt_joint_mid=0;AC_joint_nfe_XX=0;AF_joint_nfe_XX=0.00000;AN_joint_nfe_XX=25264;nhomalt_joint_nfe_XX=0;AC_joint_nfe_XY=0;AF_joint_nfe_XY=0.00000;AN_joint_nfe_XY=18184;nhomalt_joint_nfe_XY=0;AC_joint_nfe=0;AF_joint_nfe=0.00000;AN_joint_nfe=43448;nhomalt_joint_nfe=0;AC_joint_raw=1;AF_joint_raw=7.39601e-06;AN_joint_raw=135208;nhomalt_joint_raw=0;AC_joint_remaining_XX=0;AF_joint_remaining_XX=0.00000;AN_joint_remaining_XX=656;nhomalt_joint_remaining_XX=0;AC_joint_remaining_XY=0;AF_joint_remaining_XY=0.00000;AN_joint_remaining_XY=624;nhomalt_joint_remaining_XY=0;AC_joint_remaining=0;AF_joint_remaining=0.00000;AN_joint_remaining=1280;nhomalt_joint_remaining=0;AC_joint_sas_XX=0;AF_joint_sas_XX=0.00000;AN_joint_sas_XX=776;nhomalt_joint_sas_XX=0;AC_joint_sas_XY=0;AF_joint_sas_XY=0.00000;AN_joint_sas_XY=2320;nhomalt_joint_sas_XY=0;AC_joint_sas=0;AF_joint_sas=0.00000;AN_joint_sas=3096;nhomalt_joint_sas=0;faf95_joint=0.00000;faf99_joint=0.00000;faf95_joint_afr=0.00000;faf99_joint_afr=0.00000;faf95_joint_amr=0.00000;faf99_joint_amr=0.00000;faf95_joint_eas=0.00000;faf99_joint_eas=0.00000;faf95_joint_mid=0.00000;faf99_joint_mid=0.00000;faf95_joint_nfe=0.00000;faf99_joint_nfe=0.00000;faf95_joint_sas=0.00000;faf99_joint_sas=0.00000;age_hist_het_bin_freq_joint=0|0|0|0|0|0|0|0|0|0;age_hist_het_n_smaller_joint=0;age_hist_het_n_larger_joint=0;age_hist_hom_bin_freq_joint=0|0|0|0|0|0|0|0|0|0;age_hist_hom_n_smaller_joint=0;age_hist_hom_n_larger_joint=0;gq_hist_alt_bin_freq_joint=0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;gq_hist_all_bin_freq_joint=0|0|0|0|29875|7371|5291|2687|1255|1172|799|403|450|325|152|182|138|50|77|151;dp_hist_alt_bin_freq_joint=0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;dp_hist_alt_n_larger_joint=0;dp_hist_all_bin_freq_joint=0|0|11627|15622|9366|6140|4410|1795|665|307|189|96|70|37|20|14|8|4|2|3;dp_hist_all_n_larger_joint=3;ab_hist_alt_bin_freq_joint=0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;outside_broad_capture_region;outside_ukb_capture_region;outside_broad_calling_region;outside_ukb_calling_region;not_called_in_exomes;AC_genomes_XX=0;AF_genomes_XX=0.00000;AN_genomes_XX=52314;nhomalt_genomes_XX=0;AC_genomes_XY=0;AF_genomes_XY=0.00000;AN_genomes_XY=48442;nhomalt_genomes_XY=0;nhomalt_genomes=0;AC_genomes_afr_XX=0;AF_genomes_afr_XX=0.00000;AN_genomes_afr_XX=16804;nhomalt_genomes_afr_XX=0;AC_genomes_afr_XY=0;AF_genomes_afr_XY=0.00000;AN_genomes_afr_XY=14556;nhomalt_genomes_afr_XY=0;AC_genomes_afr=0;AF_genomes_afr=0.00000;AN_genomes_afr=31360;nhomalt_genomes_afr=0;AC_genomes_ami_XX=0;AF_genomes_ami_XX=0.00000;AN_genomes_ami_XX=274;nhomalt_genomes_ami_XX=0;AC_genomes_ami_XY=0;AF_genomes_ami_XY=0.00000;AN_genomes_ami_XY=294;nhomalt_genomes_ami_XY=0;AC_genomes_ami=0;AF_genomes_ami=0.00000;AN_genomes_ami=568;nhomalt_genomes_ami=0;AC_genomes_amr_XX=0;AF_genomes_amr_XX=0.00000;AN_genomes_amr_XX=4074;nhomalt_genomes_amr_XX=0;AC_genomes_amr_XY=0;AF_genomes_amr_XY=0.00000;AN_genomes_amr_XY=4908;nhomalt_genomes_amr_XY=0;AC_genomes_amr=0;AF_genomes_amr=0.00000;AN_genomes_amr=8982;nhomalt_genomes_amr=0;AC_genomes_asj_XX=0;AF_genomes_asj_XX=0.00000;AN_genomes_asj_XX=1228;nhomalt_genomes_asj_XX=0;AC_genomes_asj_XY=0;AF_genomes_asj_XY=0.00000;AN_genomes_asj_XY=1078;nhomalt_genomes_asj_XY=0;AC_genomes_asj=0;AF_genomes_asj=0.00000;AN_genomes_asj=2306;nhomalt_genomes_asj=0;AC_genomes_eas_XX=0;AF_genomes_eas_XX=0.00000;AN_genomes_eas_XX=1850;nhomalt_genomes_eas_XX=0;AC_genomes_eas_XY=0;AF_genomes_eas_XY=0.00000;AN_genomes_eas_XY=2256;nhomalt_genomes_eas_XY=0;AC_genomes_eas=0;AF_genomes_eas=0.00000;AN_genomes_eas=4106;nhomalt_genomes_eas=0;AC_genomes_fin_XX=0;AF_genomes_fin_XX=0.00000;AN_genomes_fin_XX=1292;nhomalt_genomes_fin_XX=0;AC_genomes_fin_XY=0;AF_genomes_fin_XY=0.00000;AN_genomes_fin_XY=4124;nhomalt_genomes_fin_XY=0;AC_genomes_fin=0;AF_genomes_fin=0.00000;AN_genomes_fin=5416;nhomalt_genomes_fin=0;AC_genomes_mid_XX=0;AF_genomes_mid_XX=0.00000;AN_genomes_mid_XX=96;nhomalt_genomes_mid_XX=0;AC_genomes_mid_XY=0;AF_genomes_mid_XY=0.00000;AN_genomes_mid_XY=98;nhomalt_genomes_mid_XY=0;AC_genomes_mid=0;AF_genomes_mid=0.00000;AN_genomes_mid=194;nhomalt_genomes_mid=0;AC_genomes_nfe_XX=0;AF_genomes_nfe_XX=0.00000;AN_genomes_nfe_XX=25264;nhomalt_genomes_nfe_XX=0;AC_genomes_nfe_XY=0;AF_genomes_nfe_XY=0.00000;AN_genomes_nfe_XY=18184;nhomalt_genomes_nfe_XY=0;AC_genomes_nfe=0;AF_genomes_nfe=0.00000;AN_genomes_nfe=43448;nhomalt_genomes_nfe=0;AC_genomes_raw=1;AF_genomes_raw=7.39601e-06;AN_genomes_raw=135208;nhomalt_genomes_raw=0;AC_genomes_remaining_XX=0;AF_genomes_remaining_XX=0.00000;AN_genomes_remaining_XX=656;nhomalt_genomes_remaining_XX=0;AC_genomes_remaining_XY=0;AF_genomes_remaining_XY=0.00000;AN_genomes_remaining_XY=624;nhomalt_genomes_remaining_XY=0;AC_genomes_remaining=0;AF_genomes_remaining=0.00000;AN_genomes_remaining=1280;nhomalt_genomes_remaining=0;AC_genomes_sas_XX=0;AF_genomes_sas_XX=0.00000;AN_genomes_sas_XX=776;nhomalt_genomes_sas_XX=0;AC_genomes_sas_XY=0;AF_genomes_sas_XY=0.00000;AN_genomes_sas_XY=2320;nhomalt_genomes_sas_XY=0;AC_genomes_sas=0;AF_genomes_sas=0.00000;AN_genomes_sas=3096;nhomalt_genomes_sas=0;faf95_genomes=0.00000;faf99_genomes=0.00000;faf95_genomes_afr=0.00000;faf99_genomes_afr=0.00000;faf95_genomes_amr=0.00000;faf99_genomes_amr=0.00000;faf95_genomes_eas=0.00000;faf99_genomes_eas=0.00000;faf95_genomes_nfe=0.00000;faf99_genomes_nfe=0.00000;faf95_genomes_sas=0.00000;faf99_genomes_sas=0.00000;age_hist_het_bin_freq_genomes=0|0|0|0|0|0|0|0|0|0;age_hist_het_n_smaller_genomes=0;age_hist_het_n_larger_genomes=0;age_hist_hom_bin_freq_genomes=0|0|0|0|0|0|0|0|0|0;age_hist_hom_n_smaller_genomes=0;age_hist_hom_n_larger_genomes=0;gq_hist_alt_bin_freq_genomes=0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;gq_hist_all_bin_freq_genomes=0|0|0|0|29875|7371|5291|2687|1255|1172|799|403|450|325|152|182|138|50|77|151;dp_hist_alt_bin_freq_genomes=0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;dp_hist_alt_n_larger_genomes=0;dp_hist_all_bin_freq_genomes=0|0|11627|15622|9366|6140|4410|1795|665|307|189|96|70|37|20|14|8|4|2|3;dp_hist_all_n_larger_genomes=3;ab_hist_alt_bin_freq_genomes=0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0
```
I can’t comment on how pytabix or external tools are parsing gnomAD data; our team recommends using [Hail](https://hail.is/) and our [Hail utilities for gnomAD](https://github.com/broadinstitute/gnomad_methods) to parse gnomAD data.