Interim display. This page is a temporary, independent display of gnomAD Canada v1.0 data, offered until the gnomAD Canada team releases its own browser; it is not the official source. Data are provided as is, without any warranty of accuracy or completeness, and may contain errors or omissions. Verify results against the official dataset from BCGSC (bcgsc.ca/gnomad) before relying on them. For research and educational use only; not for clinical decision-making. Interim display. Not the official source; data provided as is. Verify against BCGSC.
Home / CYP2C19 c.681G>A / gnomAD Canada
gnomAD Canada v1.0 · HostSeq
NM_000769.4:c.681G>A
NP_000760.1:p.(Pro227=)  ·  CYP2C19
GRCh38
chr10:94,781,859 G>A
GRCh37
chr10:96541616 G>A
rsID
—
Type
SNV · synonymous variant
Allele type
snv · 1 alt
Cohort
HostSeq (10,487 genomes)
Flags
PASS
Allele frequency
17.2249%
3168 / 18,392 alleles
PASS
Allele count
3168
adjusted · raw: 3176
Allele number
18,392
adjusted · raw: 18,422
Allele frequency
1.72e-01
17.2249% MAF
Homozygotes
313
alt hom carriers
grpmax FAF95
3.07e-01
South Asian · AC=451 AN=1,358
FAF95 max
3.07e-01
South Asian
FAF99 max
2.97e-01
South Asian
Cohort size
10,487
whole genomes
Raw vs adjusted allele counts
ACANAFHom
Adjusted
PASS genotypes only
 316818,392 1.72e-01 313
Raw
all genotypes
 3176 18,422 1.72e-01 —
Allele frequency by ancestry
GRCh38 · HostSeq genomes · Canada
Population AC AN AF Hom
African/African American
afr
 171 1,018
16.7976%
 9
Latino/Admixed American
amr
 84 838
10.0239%
 5
Ashkenazi Jewish
asj
 106 830
12.7711%
 5
East Asian
eas
 425 1,334
31.8591%
 65
European (Finnish)
fin
 2 8
25.0000%
 1
Middle Eastern
mid
 13 144
9.0278%
 1
European (non-Finnish)
nfe
 1754 11,730
14.9531%
 139
Remaining individuals
oth
 162 1,132
14.3110%
 16
South Asiangrpmax
sas
 451 1,358
33.2106%
 72
Total
 3168 18,392
17.2249%
 313
Population codes are displayed as sourced from gnomAD Canada v1.0 without relabelling. Bar widths scaled relative to the grpmax population (South Asian). Grpmax FAF95 = 3.07e-01.
Filtering allele frequency (FAF)
PopulationFAF 95%FAF 99%
Overall
 1.67e-01 1.65e-01
African/African American
afr
 1.47e-01 1.40e-01
Latino/Admixed American
amr
 8.30e-02 7.66e-02
East Asian
eas
 2.94e-01 2.84e-01
European (non-Finnish)
nfe
 1.44e-01 1.41e-01
South Asian
sas
 3.07e-01 2.97e-01
Sex-stratified allele counts are based on inferred chromosomal sex (XX / XY) from coverage of sex chromosomes in the HostSeq cohort.
XX genotypes
1820 / 10,582  ·  17.1990%
PopulationACANAFHom
African/African American
afr
 82 552 14.855% 4
Latino/Admixed American
amr
 55 456 12.061% 3
Ashkenazi Jewish
asj
 57 420 13.571% 3
East Asian
eas
 240 744 32.258% 38
European (Finnish)
fin
 2 8 25.000% 1
Middle Eastern
mid
 6 68 8.824% 0
European (non-Finnish)
nfe
 1090 7,106 15.339% 88
Remaining individuals
oth
 83 606 13.696% 7
South Asian
sas
 205 622 32.958% 32
XY genotypes
1348 / 7,810  ·  17.2599%
PopulationACANAFHom
African/African American
afr
 89 466 19.099% 5
Latino/Admixed American
amr
 29 382 7.592% 2
Ashkenazi Jewish
asj
 49 410 11.951% 2
East Asian
eas
 185 590 31.356% 27
European (Finnish)
fin
 0 — — 0
Middle Eastern
mid
 7 76 9.211% 1
European (non-Finnish)
nfe
 664 4,624 14.360% 51
Remaining individuals
oth
 79 526 15.019% 9
South Asian
sas
 246 736 33.424% 40
Variant quality scores
MQ
Mapping quality
246.5307
FS
Fisher strand bias · lower = better
0.0
MQRankSum
MQ rank sum test
0.0
SOR
Strand odds ratio
0.6919
ReadPosRankSum
Read position rank sum
0.059
AS_pab_max
Max posterior allele balance
1.0
RF
Random forest score
0.3124
InbreedingCoeff
Inbreeding coefficient
0.0314
Region flags
LCR (low complexity region) segdup (segmental duplication) monoallelic
Allele balance · alt carriers
Allele balance distribution for alt carriers.
Expected heterozygous AB ≈ 0.5. Values near 0 or 1 may indicate homozygosity or data quality issues.
Read depth distribution (all genotypes)
Read depth distribution across all genotypes.
Genotype quality distribution
Genotype quality distribution across all genotypes.
Strand bias table (SB)
ForwardReverse
Reference
 31227 26512
Alternate
 39375 33473
Genotype quality · alt carriers only
GQ distribution for alt allele carriers.
Alt-carrier GQ distribution. High GQ (≥20) indicates confident heterozygous calls.
Read depth · alt carriers only
Depth distribution for alt allele carriers.
Applied filters
PASS singleton was_split
Age at recruitment for heterozygous carriers observed in the HostSeq cohort. Age data is available only for a subset of participants.
Age distribution · heterozygous carriers
Age distribution for heterozygous carriers.
Carriers below age 30: 430 Carriers above age 80: 159
Age distribution · homozygous carriers
Age distribution for homozygous carriers.
Dataset information
Dataset name
gnomAD Canada v1.0
Cohort
HostSeq
Data type
Whole genome sequencing
Reference genome
GRCh38
Total genomes
10,487
Alleles (this variant)
18,392
Alt allele count
3168
Homozygotes
313
Cross-reference links
gnomAD v4.1 (global) gnomad.broadinstitute.org
gnomAD v2.1 (exome) gnomad.broadinstitute.org
ClinVar — NM_000769.4:c.681G>A ncbi.nlm.nih.gov
Variant interpretation (LYFE Sciences) Back to full report
Acknowledgements & data use
Required attribution · gnomAD Canada v1.0
About this display
LYFE Sciences is an independent, unfunded variant interpretation tool. This page displays population frequency data from gnomAD Canada v1.0; I did not generate, fund, or contribute to this dataset. All data belongs to the gnomAD Canada project and the HostSeq cohort. I am presenting it in a convenient format alongside variant interpretation.
Data source
All population frequency data on this page originates from gnomAD Canada v1.0, produced from the HostSeq whole-genome sequencing cohort and made publicly available by the BC Genome Sciences Centre (BCGSC). The official gnomAD Canada browser is at gnomad.ca and the BCGSC instance at bcgsc.ca/gnomad. Please cite the original resource if you use this data in research.
Population labels
Population ancestry labels are reproduced exactly as provided by gnomAD Canada and the HostSeq cohort. These labels reflect ancestry inference using gnomAD v4 reference population PCA and are governed by the Indigenous data sovereignty principles of the Silent Genomes Project and the Indigenous Background Variant Library (IBVL).
Key references
1
Yoo S et al. HostSeq: a Canadian whole genome sequencing and clinical data resource. BMC Genom Data. 2023. doi:10.1186/s12863-023-01128-3
2
Chen S*, Francioli LC* et al. A genomic mutational constraint map using variation in 76,156 human genomes. Nature. 625, 92–100 (2024). doi:10.1038/s41586-023-06045-0