Home / DICER1 c.4206+9del / gnomAD Canada
gnomAD Canada v1.0 · HostSeq
NM_177438.3:c.4206+9del
NP_803187.1:p.?  ·  DICER1
GRCh38
chr14:95,099,770 AC>A
GRCh37
chr14:95566107 AC>A
rsID
rs368080354
Type
INDEL · intron variant
Allele type
del · 1 alt
Cohort
HostSeq (10,487 genomes)
Flags
lcr, was_split, InbreedingCoeff
Allele frequency
46.4756%
2967 / 6,384 alleles
lcr PASS
Allele count
2967
adjusted · raw: 3008
Allele number
6,384
adjusted · raw: 6,520
Allele frequency
4.65e-01
46.4756% MAF
Homozygotes
279
alt hom carriers
grpmax FAF95
4.86e-01
South Asian · AC=336 AN=630
FAF95 max
4.86e-01
South Asian
FAF99 max
4.68e-01
South Asian
Cohort size
10,487
whole genomes
Raw vs adjusted allele counts
ACANAFHom
Adjusted
PASS genotypes only
 29676,384 4.65e-01 279
Raw
all genotypes
 3008 6,520 4.61e-01 —
Allele frequency by ancestry
GRCh38 · HostSeq genomes · Canada
Population AC AN AF Hom
African/African American
afr
 370 720
51.3889%
 61
Latino/Admixed American
amr
 188 374
50.2674%
 17
Ashkenazi Jewish
asj
 102 272
37.5000%
 8
East Asian
eas
 246 464
53.0172%
 15
European (Finnish)
fin
 1 4
25.0000%
 0
Middle Eastern
mid
 21 52
40.3846%
 1
European (non-Finnish)
nfe
 1542 3,494
44.1328%
 122
Remaining individuals
oth
 161 374
43.0481%
 15
South Asiangrpmax
sas
 336 630
53.3333%
 40
Total
 2967 6,384
46.4756%
 279
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 = 4.86e-01.
Filtering allele frequency (FAF)
PopulationFAF 95%FAF 99%
Overall
 4.51e-01 4.45e-01
African/African American
afr
 4.71e-01 4.54e-01
Latino/Admixed American
amr
 4.44e-01 4.21e-01
East Asian
eas
 4.76e-01 4.55e-01
European (non-Finnish)
nfe
 4.23e-01 4.16e-01
South Asian
sas
 4.86e-01 4.68e-01
Sex-stratified allele counts are based on inferred chromosomal sex (XX / XY) from coverage of sex chromosomes in the HostSeq cohort.
XX genotypes
1626 / 3,566  ·  45.5973%
PopulationACANAFHom
African/African American
afr
 199 372 53.495% 36
Latino/Admixed American
amr
 101 208 48.558% 7
Ashkenazi Jewish
asj
 41 126 32.540% 2
East Asian
eas
 148 284 52.113% 6
European (Finnish)
fin
 1 4 25.000% 0
Middle Eastern
mid
 11 26 42.308% 1
European (non-Finnish)
nfe
 890 2,072 42.954% 62
Remaining individuals
oth
 87 192 45.312% 8
South Asian
sas
 148 282 52.482% 19
XY genotypes
1341 / 2,818  ·  47.5869%
PopulationACANAFHom
African/African American
afr
 171 348 49.138% 25
Latino/Admixed American
amr
 87 166 52.410% 10
Ashkenazi Jewish
asj
 61 146 41.781% 6
East Asian
eas
 98 180 54.444% 9
European (Finnish)
fin
 0 — — 0
Middle Eastern
mid
 10 26 38.462% 0
European (non-Finnish)
nfe
 652 1,422 45.851% 60
Remaining individuals
oth
 74 182 40.659% 7
South Asian
sas
 188 348 54.023% 21
Variant quality scores
MQ
Mapping quality
248.7962
FS
Fisher strand bias · lower = better
0.0
MQRankSum
MQ rank sum test
0.0
SOR
Strand odds ratio
0.6824
ReadPosRankSum
Read position rank sum
0.382
AS_pab_max
Max posterior allele balance
1.0
RF
Random forest score
0.9147
InbreedingCoeff
Inbreeding coefficient
-0.4948
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
 6795 5475
Alternate
 46002 37471
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
InbreedingCoeff 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: 420 Carriers above age 80: 145
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)
6,384
Alt allele count
2967
Homozygotes
279
Cross-reference links
gnomAD v4.1 (global) gnomad.broadinstitute.org
gnomAD v2.1 (exome) gnomad.broadinstitute.org
ClinVar — NM_177438.3:c.4206+9del 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