Home / MBD4 c.1543+14C>T / gnomAD Canada
gnomAD Canada v1.0 · HostSeq
NM_001276270.2:c.1543+14C>T
NP_001263199.1:p.?  ·  MBD4
GRCh38
chr3:129,433,084 G>A
GRCh37
chr3:129151927 G>A
rsID
rs140697
Type
MULTI-SNV · splice region variant
Allele type
snv · 3 alt
Cohort
HostSeq (10,487 genomes)
Flags
was_split
Allele frequency
18.2880%
3365 / 18,400 alleles
PASS
Allele count
3365
adjusted · raw: 3372
Allele number
18,400
adjusted · raw: 18,422
Allele frequency
1.83e-01
18.2880% MAF
Homozygotes
464
alt hom carriers
grpmax FAF95
4.58e-01
African/African American · AC=503 AN=1,018
FAF95 max
4.58e-01
African/African American
FAF99 max
4.44e-01
African/African American
Cohort size
10,487
whole genomes
Raw vs adjusted allele counts
ACANAFHom
Adjusted
PASS genotypes only
 336518,400 1.83e-01 464
Raw
all genotypes
 3372 18,422 1.83e-01 —
Allele frequency by ancestry
GRCh38 · HostSeq genomes · Canada
Population AC AN AF Hom
African/African Americangrpmax
afr
 503 1,018
49.4106%
 130
Latino/Admixed American
amr
 191 838
22.7924%
 18
Ashkenazi Jewish
asj
 123 830
14.8193%
 13
East Asian
eas
 645 1,338
48.2063%
 157
European (Finnish)
fin
 0 8 — 0
Middle Eastern
mid
 27 144
18.7500%
 0
European (non-Finnish)
nfe
 1226 11,730
10.4518%
 67
Remaining individuals
oth
 256 1,134
22.5750%
 30
South Asian
sas
 394 1,360
28.9706%
 49
Total
 3365 18,400
18.2880%
 464
Population codes are displayed as sourced from gnomAD Canada v1.0 without relabelling. Bar widths scaled relative to the grpmax population (African/African American). Grpmax FAF95 = 4.58e-01.
Filtering allele frequency (FAF)
PopulationFAF 95%FAF 99%
Overall
 1.78e-01 1.76e-01
African/African American
afr
 4.58e-01 4.44e-01
Latino/Admixed American
amr
 2.01e-01 1.91e-01
East Asian
eas
 4.51e-01 4.39e-01
European (non-Finnish)
nfe
 9.97e-02 9.77e-02
South Asian
sas
 2.66e-01 2.57e-01
Sex-stratified allele counts are based on inferred chromosomal sex (XX / XY) from coverage of sex chromosomes in the HostSeq cohort.
XX genotypes
1854 / 10,582  ·  17.5203%
PopulationACANAFHom
African/African American
afr
 264 550 48.000% 62
Latino/Admixed American
amr
 102 456 22.368% 7
Ashkenazi Jewish
asj
 61 418 14.593% 8
East Asian
eas
 354 746 47.453% 84
European (Finnish)
fin
 0 8 — 0
Middle Eastern
mid
 16 68 23.529% 0
European (non-Finnish)
nfe
 728 7,102 10.251% 35
Remaining individuals
oth
 152 610 24.918% 23
South Asian
sas
 177 624 28.365% 19
XY genotypes
1511 / 7,818  ·  19.3272%
PopulationACANAFHom
African/African American
afr
 239 468 51.068% 68
Latino/Admixed American
amr
 89 382 23.298% 11
Ashkenazi Jewish
asj
 62 412 15.049% 5
East Asian
eas
 291 592 49.155% 73
European (Finnish)
fin
 0 — — 0
Middle Eastern
mid
 11 76 14.474% 0
European (non-Finnish)
nfe
 498 4,628 10.761% 32
Remaining individuals
oth
 104 524 19.847% 7
South Asian
sas
 217 736 29.484% 30
Variant quality scores
MQ
Mapping quality
249.8457
FS
Fisher strand bias · lower = better
0.0
MQRankSum
MQ rank sum test
0.0
SOR
Strand odds ratio
0.692
ReadPosRankSum
Read position rank sum
0.044
AS_pab_max
Max posterior allele balance
1.0
RF
Random forest score
0.9529
InbreedingCoeff
Inbreeding coefficient
0.1135
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
 32648 28006
Alternate
 45287 38891
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: 477 Carriers above age 80: 137
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
3365
Homozygotes
464
Cross-reference links
gnomAD v4.1 (global) gnomad.broadinstitute.org
gnomAD v2.1 (exome) gnomad.broadinstitute.org
ClinVar — NM_001276270.2:c.1543+14C>T 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