Home / CCND1 c.723G>A / gnomAD Canada
gnomAD Canada v1.0 · HostSeq
NM_053056.3:c.723G>A
NP_444284.1:p.(Pro241=)  ·  CCND1
GRCh38
chr11:69,648,142 G>A
GRCh37
chr11:69462910 G>A
rsID
rs9344
Type
MIXED · splice region variant
Allele type
snv · 2 alt
Cohort
HostSeq (10,487 genomes)
Flags
was_split
Allele frequency
46.6082%
8561 / 18,368 alleles
PASS
Allele count
8561
adjusted · raw: 8597
Allele number
18,368
adjusted · raw: 18,422
Allele frequency
4.66e-01
46.6082% MAF
Homozygotes
2065
alt hom carriers
grpmax FAF95
5.40e-01
East Asian · AC=766 AN=1,336
FAF95 max
5.40e-01
East Asian
FAF99 max
5.26e-01
East Asian
Cohort size
10,487
whole genomes
Raw vs adjusted allele counts
ACANAFHom
Adjusted
PASS genotypes only
 856118,368 4.66e-01 2065
Raw
all genotypes
 8597 18,422 4.67e-01 —
Allele frequency by ancestry
GRCh38 · HostSeq genomes · Canada
Population AC AN AF Hom
African/African American
afr
 237 1,018
23.2809%
 21
Latino/Admixed American
amr
 324 836
38.7560%
 66
Ashkenazi Jewish
asj
 395 832
47.4760%
 88
East Asiangrpmax
eas
 766 1,336
57.3353%
 227
European (Finnish)
fin
 4 8
50.0000%
 1
Middle Eastern
mid
 80 144
55.5556%
 20
European (non-Finnish)
nfe
 5495 11,700
46.9658%
 1313
Remaining individuals
oth
 569 1,132
50.2650%
 144
South Asian
sas
 691 1,362
50.7342%
 185
Total
 8561 18,368
46.6082%
 2065
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 = 5.40e-01.
Filtering allele frequency (FAF)
PopulationFAF 95%FAF 99%
Overall
 4.58e-01 4.54e-01
African/African American
afr
 2.09e-01 1.99e-01
Latino/Admixed American
amr
 3.53e-01 3.39e-01
East Asian
eas
 5.40e-01 5.26e-01
European (non-Finnish)
nfe
 4.59e-01 4.55e-01
South Asian
sas
 4.76e-01 4.64e-01
Sex-stratified allele counts are based on inferred chromosomal sex (XX / XY) from coverage of sex chromosomes in the HostSeq cohort.
XX genotypes
4871 / 10,562  ·  46.1182%
PopulationACANAFHom
African/African American
afr
 131 550 23.818% 13
Latino/Admixed American
amr
 192 456 42.105% 44
Ashkenazi Jewish
asj
 188 420 44.762% 36
East Asian
eas
 420 744 56.452% 129
European (Finnish)
fin
 4 8 50.000% 1
Middle Eastern
mid
 32 68 47.059% 8
European (non-Finnish)
nfe
 3287 7,086 46.387% 781
Remaining individuals
oth
 305 604 50.497% 80
South Asian
sas
 312 626 49.840% 84
XY genotypes
3690 / 7,806  ·  47.2713%
PopulationACANAFHom
African/African American
afr
 106 468 22.650% 8
Latino/Admixed American
amr
 132 380 34.737% 22
Ashkenazi Jewish
asj
 207 412 50.243% 52
East Asian
eas
 346 592 58.446% 98
European (Finnish)
fin
 0 — — 0
Middle Eastern
mid
 48 76 63.158% 12
European (non-Finnish)
nfe
 2208 4,614 47.854% 532
Remaining individuals
oth
 264 528 50.000% 64
South Asian
sas
 379 736 51.495% 101
Variant quality scores
MQ
Mapping quality
249.8068
FS
Fisher strand bias · lower = better
0.0
MQRankSum
MQ rank sum test
0.0
SOR
Strand odds ratio
0.6875
ReadPosRankSum
Read position rank sum
0.0
AS_pab_max
Max posterior allele balance
1.0
RF
Random forest score
0.9478
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
 64137 53127
Alternate
 124124 103397
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: 757 Carriers above age 80: 262
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)
18,368
Alt allele count
8561
Homozygotes
2065
Cross-reference links
gnomAD v4.1 (global) gnomad.broadinstitute.org
gnomAD v2.1 (exome) gnomad.broadinstitute.org
ClinVar — NM_053056.3:c.723G>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