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 / SLCO1B1 c.521T>C / gnomAD Canada
gnomAD Canada v1.0 · HostSeq
NM_006446.5:c.521T>C
NP_006437.3:p.(Val174Ala)  ·  SLCO1B1
GRCh38
chr12:21,178,615 T>C
GRCh37
chr12:21331549 T>C
rsID
rs4149056
Type
MULTI-SNV · missense variant
Allele type
snv · 2 alt
Cohort
HostSeq (10,487 genomes)
Flags
was_split
Allele frequency
14.8261%
2728 / 18,400 alleles
PASS
Allele count
2728
adjusted · raw: 2737
Allele number
18,400
adjusted · raw: 18,422
Allele frequency
1.48e-01
14.8261% MAF
Homozygotes
222
alt hom carriers
grpmax FAF95
1.66e-01
European (non-Finnish) · AC=2019 AN=11,724
FAF95 max
1.66e-01
European (non-Finnish)
FAF99 max
1.63e-01
European (non-Finnish)
Cohort size
10,487
whole genomes
Raw vs adjusted allele counts
ACANAFHom
Adjusted
PASS genotypes only
 272818,400 1.48e-01 222
Raw
all genotypes
 2737 18,422 1.49e-01 —
Allele frequency by ancestry
GRCh38 · HostSeq genomes · Canada
Population AC AN AF Hom
African/African American
afr
 29 1,020
2.8431%
 1
Latino/Admixed American
amr
 132 838
15.7518%
 11
Ashkenazi Jewish
asj
 157 830
18.9157%
 16
East Asian
eas
 147 1,338
10.9865%
 6
European (Finnish)
fin
 0 8 — 0
Middle Eastern
mid
 24 144
16.6667%
 0
European (non-Finnish)grpmax
nfe
 2019 11,724
17.2211%
 174
Remaining individuals
oth
 161 1,136
14.1725%
 12
South Asian
sas
 59 1,362
4.3319%
 2
Total
 2728 18,400
14.8261%
 222
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 = 1.66e-01.
Filtering allele frequency (FAF)
PopulationFAF 95%FAF 99%
Overall
 1.44e-01 1.42e-01
African/African American
afr
 2.03e-02 1.76e-02
Latino/Admixed American
amr
 1.36e-01 1.27e-01
East Asian
eas
 9.54e-02 8.99e-02
European (non-Finnish)
nfe
 1.66e-01 1.63e-01
South Asian
sas
 3.45e-02 3.13e-02
Sex-stratified allele counts are based on inferred chromosomal sex (XX / XY) from coverage of sex chromosomes in the HostSeq cohort.
XX genotypes
1605 / 10,578  ·  15.1730%
PopulationACANAFHom
African/African American
afr
 14 552 2.536% 1
Latino/Admixed American
amr
 75 456 16.447% 7
Ashkenazi Jewish
asj
 83 418 19.856% 10
East Asian
eas
 83 746 11.126% 6
European (Finnish)
fin
 0 8 — 0
Middle Eastern
mid
 11 68 16.176% 0
European (non-Finnish)
nfe
 1219 7,096 17.179% 103
Remaining individuals
oth
 86 608 14.145% 10
South Asian
sas
 34 626 5.431% 1
XY genotypes
1123 / 7,822  ·  14.3569%
PopulationACANAFHom
African/African American
afr
 15 468 3.205% 0
Latino/Admixed American
amr
 57 382 14.921% 4
Ashkenazi Jewish
asj
 74 412 17.961% 6
East Asian
eas
 64 592 10.811% 0
European (Finnish)
fin
 0 — — 0
Middle Eastern
mid
 13 76 17.105% 0
European (non-Finnish)
nfe
 800 4,628 17.286% 71
Remaining individuals
oth
 75 528 14.205% 2
South Asian
sas
 25 736 3.397% 1
Variant quality scores
MQ
Mapping quality
245.2749
FS
Fisher strand bias · lower = better
0.0
MQRankSum
MQ rank sum test
-2.46
SOR
Strand odds ratio
0.6921
ReadPosRankSum
Read position rank sum
0.028
AS_pab_max
Max posterior allele balance
1.0
RF
Random forest score
0.795
InbreedingCoeff
Inbreeding coefficient
0.016
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
 27599 27511
Alternate
 31984 32053
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: 378 Carriers above age 80: 133
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)
18,400
Alt allele count
2728
Homozygotes
222
Cross-reference links
gnomAD v4.1 (global) gnomad.broadinstitute.org
gnomAD v2.1 (exome) gnomad.broadinstitute.org
ClinVar — NM_006446.5:c.521T>C 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