Version: 3.2.5

gnomAD

Overview

The Genome Aggregation Database (gnomAD) is a resource developed by an international coalition of investigators, with the goal of aggregating and harmonizing both exome and genome sequencing data from a wide variety of large-scale sequencing projects, and making summary data available for the wider scientific community.

Small Variants

VCF extraction

We currently extract the following info fields from gnomAD genome and exome VCF files:

##INFO=<ID=AC,Number=A,Type=Integer,Description="Alternate allele count for samples">
##INFO=<ID=AN,Number=A,Type=Integer,Description="Total number of alleles in samples">
##INFO=<ID=nhomalt,Number=A,Type=Integer,Description="Count of homozygous individuals in samples">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Depth of informative coverage for each sample; reads with MQ=255 or with bad mates are filtered">
##INFO=<ID=lcr,Number=0,Type=Flag,Description="Variant falls within a low complexity region">
##INFO=<ID=AC_afr,Number=A,Type=Integer,Description="Alternate allele count for samples of African-American ancestry">
##INFO=<ID=AN_afr,Number=A,Type=Integer,Description="Total number of alleles in samples of African-American ancestry">
##INFO=<ID=AF_afr,Number=A,Type=Float,Description="Alternate allele frequency in samples of African-American ancestry">
##INFO=<ID=nhomalt_afr,Number=A,Type=Integer,Description="Count of homozygous individuals in samples of African-American ancestry">
##INFO=<ID=AC_amr,Number=A,Type=Integer,Description="Alternate allele count for samples of Latino ancestry">
##INFO=<ID=AN_amr,Number=A,Type=Integer,Description="Total number of alleles in samples of Latino ancestry">
##INFO=<ID=nhomalt_amr,Number=A,Type=Integer,Description="Count of homozygous individuals in samples of Latino ancestry">
##INFO=<ID=AC_eas,Number=A,Type=Integer,Description="Alternate allele count for samples of East Asian ancestry">
##INFO=<ID=AN_eas,Number=A,Type=Integer,Description="Total number of alleles in samples of East Asian ancestry">
##INFO=<ID=nhomalt_eas,Number=A,Type=Integer,Description="Count of homozygous individuals in samples of East Asian ancestry">
##INFO=<ID=AC_female,Number=A,Type=Integer,Description="Alternate allele count for female samples">
##INFO=<ID=AN_female,Number=A,Type=Integer,Description="Total number of alleles in female samples">
##INFO=<ID=nhomalt_female,Number=A,Type=Integer,Description="Count of homozygous individuals in female samples">
##INFO=<ID=AC_nfe,Number=A,Type=Integer,Description="Alternate allele count for samples of non-Finnish European ancestry">
##INFO=<ID=AN_nfe,Number=A,Type=Integer,Description="Total number of alleles in samples of non-Finnish European ancestry">
##INFO=<ID=nhomalt_nfe,Number=A,Type=Integer,Description="Count of homozygous individuals in samples of non-Finnish European ancestry">
##INFO=<ID=AC_fin,Number=A,Type=Integer,Description="Alternate allele count for samples of Finnish ancestry">
##INFO=<ID=AN_fin,Number=A,Type=Integer,Description="Total number of alleles in samples of Finnish ancestry">
##INFO=<ID=nhomalt_fin,Number=A,Type=Integer,Description="Count of homozygous individuals in samples of Finnish ancestry">
##INFO=<ID=AC_asj,Number=A,Type=Integer,Description="Alternate allele count for samples of Ashkenazi Jewish ancestry">
##INFO=<ID=AN_asj,Number=A,Type=Integer,Description="Total number of alleles in samples of Ashkenazi Jewish ancestry">
##INFO=<ID=nhomalt_asj,Number=A,Type=Integer,Description="Count of homozygous individuals in samples of Ashkenazi Jewish ancestry">
##INFO=<ID=AC_oth,Number=A,Type=Integer,Description="Alternate allele count for samples of uncertain ancestry">
##INFO=<ID=AN_oth,Number=A,Type=Integer,Description="Total number of alleles in samples of uncertain ancestry">
##INFO=<ID=nhomalt_oth,Number=A,Type=Integer,Description="Count of homozygous individuals in samples of uncertain ancestry">
##INFO=<ID=AC_male,Number=A,Type=Integer,Description="Alternate allele count for male samples">
##INFO=<ID=AN_male,Number=A,Type=Integer,Description="Total number of alleles in male samples">
##INFO=<ID=nhomalt_male,Number=A,Type=Integer,Description="Count of homozygous individuals in male samples">
##INFO=<ID=controls_AC,Number=A,Type=Integer,Description="Alternate allele count for samples in the controls subset">
##INFO=<ID=controls_AN,Number=A,Type=Integer,Description="Total number of alleles in samples in the controls subset">

We also extract the following extra fields from gnomAD exome VCF file:

##INFO=<ID=AC_sas,Number=A,Type=Integer,Description="Alternate allele count for samples of South Asian ancestry">
##INFO=<ID=AN_sas,Number=A,Type=Integer,Description="Total number of alleles in samples of South Asian ancestry">
##INFO=<ID=nhomalt_sas,Number=A,Type=Integer,Description="Count of homozygous individuals in samples of South Asian ancestry">

Computation

Using these, we compute the following:

Coverage
Allele count, Homozygous count, allele number and allele frequencies for:
- Global population
- African/African Americans
- Admixed Americans
- Ashkenazi Jews
- East Asians
- Finnish
- Non-Finnish Europeans
- South Asian
- Others (population not assigned)
- Male
- Female
- Controls

Note

Coverage = DP / AN. Frequencies are computed using AC/AN for each population.
Please note that currently there is no genome sequencing data of south asian (SAS) population available in gnomAD.
Allele Count, Homozygous count, allele number and allele frequencies for control groups are also provided for the global population.

VCF download instructions

https://gnomad.broadinstitute.org/downloads

JSON output

Genome and exome allele frequencies are provided in separate JSON sections.

Genomes

"gnomad":{ 
   "coverage":20,
   "allAf":0.190317,
   "afrAf":0.222876,
   "amrAf":0.121394,
   "easAf":0.239802,
   "finAf":0.136833,
   "nfeAf":0.181282,
   "asjAf":0.258278,
   "othAf":0.186094,
   "allAn":30796,
   "afrAn":8664,
   "amrAn":832,
   "easAn":1618,
   "finAn":3486,
   "nfeAn":14916,
   "asjAn":302,
   "othAn":978,
   "allAc":5861,
   "afrAc":1931,
   "amrAc":101,
   "easAc":388,
   "finAc":477,
   "nfeAc":2704,
   "asjAc":78,
   "othAc":182,
   "allHc":561,
   "afrHc":208,
   "amrHc":6,
   "easHc":42,
   "finHc":31,
   "nfeHc":242,
   "asjHc":13,
   "othHc":19,
   "failedFilter":true
}

Field	Type	Notes
coverage	int	average coverage (non-negative integer values)
allAf	float	allele frequency for all populations. Range: 0 - 1.0
allAc	int	allele count for all populations. Integer.
allAn	int	allele number for all populations. Non-zero integer.
allHc	int	count of homozygous individuals for all populations. Non-negative integer.
afrAf	float	allele frequency for the African / African American population. Range: 0 - 1.0
afrAc	int	allele count for the African / African American population. Integer.
afrAn	int	allele number for the African / African American population. Non-zero integer.
afrHc	int	count of homozygous individuals for African / African American population. Non-negative integer.
amrAf	float	allele frequency for the Latino population. Range: 0 - 1.0
amrAc	int	allele count for the Latino population. Integer.
amrAn	int	allele number for the Latino population. Non-zero integer.
amrHc	int	count of homozygous individuals for Latino population. Non-negative integer.
easAf	float	allele frequency for the East Asian population. Range: 0 - 1.0
easAc	int	allele count for the East Asian population. Integer.
easAn	int	allele number for the East Asian population. Non-zero integer.
easHc	int	count of homozygous individuals for East Asian population. Non-negative integer.
finAf	float	allele frequency for the Finnish population. Range: 0 - 1.0
finAc	int	allele count for the Finnish population. Integer.
finAn	int	allele number for the Finnish population. Non-zero integer.
finHc	int	count of homozygous individuals for Finnish population. Non-negative integer
nfeAf	float	allele frequency for the Non-Finnish European population. Range: 0 - 1.0
nfeAc	int	allele count for the Non-Finnish European population. Integer.
nfeAn	int	allele number for the Non-Finnish European population. Non-zero integer.
nfeHc	int	count of homozygous individuals for Non-Finnish European population. Non-negative integer
othAf	float	allele frequency for the Other population. Range: 0 - 1.0
othAc	int	allele count for the Other population. Integer.
othAn	int	allele number for the Other population. Non-zero integer.
othHc	int	count of homozygous individuals for Other population. Non-negative integer
asjAf	float	allele frequency for the Ashkenazi Jewish population. Range: 0 - 1.0
asjAc	int	allele count for the Ashkenazi Jewish population Integer.
asjAn	int	allele number for the Ashkenazi Jewish population. Non-zero integer.
asjHc	int	count of homozygous individuals for the Ashkenazi Jewish population. Non-negative integer
failedFilter	bool	True if this variant failed any filters (Note: we do not list the failed filters)

Exomes

"gnomadExome":{ 
   "coverage":20,
   "allAf":0.190317,
   "afrAf":0.222876,
   "amrAf":0.121394,
   "easAf":0.239802,
   "finAf":0.136833,
   "nfeAf":0.181282,
   "asjAf":0.258278,
   "othAf":0.186094,
   "allAn":30796,
   "afrAn":8664,
   "amrAn":832,
   "easAn":1618,
   "finAn":3486,
   "nfeAn":14916,
   "asjAn":302,
   "othAn":978,
   "allAc":5861,
   "afrAc":1931,
   "amrAc":101,
   "easAc":388,
   "finAc":477,
   "nfeAc":2704,
   "asjAc":78,
   "othAc":182,
   "allHc":561,
   "afrHc":208,
   "amrHc":6,
   "easHc":42,
   "finHc":31,
   "nfeHc":242,
   "asjHc":13,
   "othHc":19,
   "failedFilter":true
}

Field	Type	Notes
coverage	int	average coverage (non-negative integer values)
allAf	float	allele frequency for all populations. Range: 0 - 1.0
allAc	int	allele count for all populations. Integer.
allAn	int	allele number for all populations. Non-zero integer.
allHc	int	count of homozygous individuals for all populations. Non-negative integer.
afrAf	float	allele frequency for the African / African American population. Range: 0 - 1.0
afrAc	int	allele count for the African / African American population. Integer.
afrAn	int	allele number for the African / African American population. Non-zero integer.
afrHc	int	count of homozygous individuals for African / African American population. Non-negative integer.
amrAf	float	allele frequency for the Latino population. Range: 0 - 1.0
amrAc	int	allele count for the Latino population. Integer.
amrAn	int	allele number for the Latino population. Non-zero integer.
amrHc	int	count of homozygous individuals for Latino population. Non-negative integer.
easAf	float	allele frequency for the East Asian population. Range: 0 - 1.0
easAc	int	allele count for the East Asian population. Integer.
easAn	int	allele number for the East Asian population. Non-zero integer.
easHc	int	count of homozygous individuals for East Asian population. Non-negative integer.
finAf	float	allele frequency for the Finnish population. Range: 0 - 1.0
finAc	int	allele count for the Finnish population. Integer.
finAn	int	allele number for the Finnish population. Non-zero integer.
finHc	int	count of homozygous individuals for Finnish population. Non-negative integer
nfeAf	float	allele frequency for the Non-Finnish European population. Range: 0 - 1.0
nfeAc	int	allele count for the Non-Finnish European population. Integer.
nfeAn	int	allele number for the Non-Finnish European population. Non-zero integer.
nfeHc	int	count of homozygous individuals for Non-Finnish European population. Non-negative integer
othAf	float	allele frequency for the Other population. Range: 0 - 1.0
othAc	int	allele count for the Other population. Integer.
othAn	int	allele number for the Other population. Non-zero integer.
othHc	int	count of homozygous individuals for Other population. Non-negative integer
asjAf	float	allele frequency for the Ashkenazi Jewish population. Range: 0 - 1.0
asjAc	int	allele count for the Ashkenazi Jewish population Integer.
asjAn	int	allele number for the Ashkenazi Jewish population. Non-zero integer.
asjHc	int	count of homozygous individuals for the Ashkenazi Jewish population. Non-negative integer
sasAf	float	allele frequency for the South Asian population. Range: 0 - 1.0
sasAc	int	allele count for the South Asian population Integer.
sasAn	int	allele number for the South Asian population. Non-zero integer.
sasHc	int	count of homozygous individuals for the South Asian population. Non-negative integer.
failedFilter	bool	True if this variant failed any filters (Note: we do not list the failed filters)

Overview​

Small Variants​

VCF extraction​

Computation​

Note

VCF download instructions​

JSON output​

Genomes​

Exomes​