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 / HFE c.187C>G / gnomAD Canada
gnomAD Canada v1.0 · HostSeq
NM_000410.4:c.187C>G
NP_000401.1:p.(His63Asp)  ·  HFE
GRCh38
chr6:26,090,951 C>G
GRCh37
chr6:26091179 C>G
rsID
rs1799945
Type
MULTI-SNV · missense variant
Allele type
snv · 2 alt
Cohort
HostSeq (10,487 genomes)
Flags
was_split
Allele frequency
13.5050%
2486 / 18,408 alleles
PASS
Allele count
2486
adjusted · raw: 2493
Allele number
18,408
adjusted · raw: 18,422
Allele frequency
1.35e-01
13.5050% MAF
Homozygotes
196
alt hom carriers
grpmax FAF95
1.61e-01
European (non-Finnish) · AC=1965 AN=11,730
FAF95 max
1.61e-01
European (non-Finnish)
FAF99 max
1.59e-01
European (non-Finnish)
Cohort size
10,487
whole genomes
Raw vs adjusted allele counts
ACANAFHom
Adjusted
PASS genotypes only
 248618,408 1.35e-01 196
Raw
all genotypes
 2493 18,422 1.35e-01 —
Allele frequency by ancestry
GRCh38 · HostSeq genomes · Canada
Population AC AN AF Hom
African/African American
afr
 15 1,020
1.4706%
 0
Latino/Admixed American
amr
 95 836
11.3636%
 6
Ashkenazi Jewish
asj
 102 832
12.2596%
 5
East Asian
eas
 42 1,338
3.1390%
 1
European (Finnish)
fin
 0 8 — 0
Middle Eastern
mid
 18 144
12.5000%
 1
European (non-Finnish)grpmax
nfe
 1965 11,730
16.7519%
 175
Remaining individuals
oth
 128 1,138
11.2478%
 4
South Asian
sas
 121 1,362
8.8840%
 4
Total
 2486 18,408
13.5050%
 196
Population codes are displayed as sourced from gnomAD Canada v1.0 without relabelling. Bar widths scaled relative to the grpmax population (European (non-Finnish)). Grpmax FAF95 = 1.61e-01.
Filtering allele frequency (FAF)
PopulationFAF 95%FAF 99%
Overall
 1.31e-01 1.29e-01
African/African American
afr
 9.06e-03 7.33e-03
Latino/Admixed American
amr
 9.52e-02 8.83e-02
East Asian
eas
 2.39e-02 2.12e-02
European (non-Finnish)
nfe
 1.61e-01 1.59e-01
South Asian
sas
 7.60e-02 7.11e-02
Sex-stratified allele counts are based on inferred chromosomal sex (XX / XY) from coverage of sex chromosomes in the HostSeq cohort.
XX genotypes
1441 / 10,592  ·  13.6046%
PopulationACANAFHom
African/African American
afr
 10 552 1.812% 0
Latino/Admixed American
amr
 51 456 11.184% 6
Ashkenazi Jewish
asj
 54 420 12.857% 3
East Asian
eas
 21 746 2.815% 0
European (Finnish)
fin
 0 8 — 0
Middle Eastern
mid
 8 68 11.765% 0
European (non-Finnish)
nfe
 1164 7,106 16.381% 98
Remaining individuals
oth
 68 610 11.148% 1
South Asian
sas
 65 626 10.383% 4
XY genotypes
1045 / 7,816  ·  13.3700%
PopulationACANAFHom
African/African American
afr
 5 468 1.068% 0
Latino/Admixed American
amr
 44 380 11.579% 0
Ashkenazi Jewish
asj
 48 412 11.650% 2
East Asian
eas
 21 592 3.547% 1
European (Finnish)
fin
 0 — — 0
Middle Eastern
mid
 10 76 13.158% 1
European (non-Finnish)
nfe
 801 4,624 17.323% 77
Remaining individuals
oth
 60 528 11.364% 3
South Asian
sas
 56 736 7.609% 0
Variant quality scores
MQ
Mapping quality
249.8136
FS
Fisher strand bias · lower = better
0.0
MQRankSum
MQ rank sum test
0.0
SOR
Strand odds ratio
0.7192
ReadPosRankSum
Read position rank sum
-0.029
AS_pab_max
Max posterior allele balance
1.0
RF
Random forest score
0.9529
InbreedingCoeff
Inbreeding coefficient
0.0263
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
 25811 22051
Alternate
 30809 25653
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: 317 Carriers above age 80: 152
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)
18,408
Alt allele count
2486
Homozygotes
196
Cross-reference links
gnomAD v4.1 (global) gnomad.broadinstitute.org
gnomAD v2.1 (exome) gnomad.broadinstitute.org
ClinVar — NM_000410.4:c.187C>G 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