Home / FGFR4 c.1162G>A / gnomAD Canada
gnomAD Canada v1.0 · HostSeq
NM_213647.2:c.1162G>A
NP_998812.1:p.(Gly388Arg)  ·  FGFR4
GRCh38
chr5:177,093,242 G>A
GRCh37
chr5:176520243 G>A
rsID
rs351855
Type
MULTI-SNV · missense variant
Allele type
snv · 3 alt
Cohort
HostSeq (10,487 genomes)
Flags
was_split
Allele frequency
30.6672%
5644 / 18,404 alleles
PASS
Allele count
5644
adjusted · raw: 5657
Allele number
18,404
adjusted · raw: 18,422
Allele frequency
3.07e-01
30.6672% MAF
Homozygotes
883
alt hom carriers
grpmax FAF95
4.45e-01
East Asian · AC=636 AN=1,338
FAF95 max
4.45e-01
East Asian
FAF99 max
4.33e-01
East Asian
Cohort size
10,487
whole genomes
Raw vs adjusted allele counts
ACANAFHom
Adjusted
PASS genotypes only
 564418,404 3.07e-01 883
Raw
all genotypes
 5657 18,422 3.07e-01 —
Allele frequency by ancestry
GRCh38 · HostSeq genomes · Canada
Population AC AN AF Hom
African/African American
afr
 122 1,020
11.9608%
 9
Latino/Admixed American
amr
 286 836
34.2105%
 48
Ashkenazi Jewish
asj
 256 832
30.7692%
 36
East Asiangrpmax
eas
 636 1,338
47.5336%
 150
European (Finnish)
fin
 1 8
12.5000%
 0
Middle Eastern
mid
 31 142
21.8310%
 1
European (non-Finnish)
nfe
 3474 11,730
29.6164%
 498
Remaining individuals
oth
 343 1,138
30.1406%
 54
South Asian
sas
 495 1,360
36.3971%
 87
Total
 5644 18,404
30.6672%
 883
Population codes are displayed as sourced from gnomAD Canada v1.0 without relabelling. Bar widths scaled relative to the grpmax population (East Asian). Grpmax FAF95 = 4.45e-01.
Filtering allele frequency (FAF)
PopulationFAF 95%FAF 99%
Overall
 3.00e-01 2.97e-01
African/African American
afr
 1.02e-01 9.59e-02
Latino/Admixed American
amr
 3.10e-01 2.97e-01
East Asian
eas
 4.45e-01 4.33e-01
European (non-Finnish)
nfe
 2.88e-01 2.85e-01
South Asian
sas
 3.37e-01 3.27e-01
Sex-stratified allele counts are based on inferred chromosomal sex (XX / XY) from coverage of sex chromosomes in the HostSeq cohort.
XX genotypes
3272 / 10,588  ·  30.9029%
PopulationACANAFHom
African/African American
afr
 70 552 12.681% 2
Latino/Admixed American
amr
 152 456 33.333% 26
Ashkenazi Jewish
asj
 119 420 28.333% 15
East Asian
eas
 343 746 45.979% 74
European (Finnish)
fin
 1 8 12.500% 0
Middle Eastern
mid
 17 66 25.758% 1
European (non-Finnish)
nfe
 2145 7,104 30.194% 302
Remaining individuals
oth
 201 610 32.951% 34
South Asian
sas
 224 626 35.783% 38
XY genotypes
2372 / 7,816  ·  30.3480%
PopulationACANAFHom
African/African American
afr
 52 468 11.111% 7
Latino/Admixed American
amr
 134 380 35.263% 22
Ashkenazi Jewish
asj
 137 412 33.252% 21
East Asian
eas
 293 592 49.493% 76
European (Finnish)
fin
 0 — — 0
Middle Eastern
mid
 14 76 18.421% 0
European (non-Finnish)
nfe
 1329 4,626 28.729% 196
Remaining individuals
oth
 142 528 26.894% 20
South Asian
sas
 271 734 36.921% 49
Variant quality scores
MQ
Mapping quality
242.9913
FS
Fisher strand bias · lower = better
0.0
MQRankSum
MQ rank sum test
-0.094
SOR
Strand odds ratio
0.677
ReadPosRankSum
Read position rank sum
0.019
AS_pab_max
Max posterior allele balance
1.0
RF
Random forest score
0.7954
InbreedingCoeff
Inbreeding coefficient
0.0099
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
 52099 50883
Alternate
 75166 74616
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: 688 Carriers above age 80: 235
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)
18,404
Alt allele count
5644
Homozygotes
883
Cross-reference links
gnomAD v4.1 (global) gnomad.broadinstitute.org
gnomAD v2.1 (exome) gnomad.broadinstitute.org
ClinVar — NM_213647.2:c.1162G>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