Home / MBD4 c.1395C>T / gnomAD Canada
gnomAD Canada v1.0 · HostSeq
NM_001276270.2:c.1395C>T
NP_001263199.1:p.(Gly465=)  ·  MBD4
GRCh38
chr3:129,433,246 G>A
GRCh37
chr3:129152089 G>A
rsID
—
Type
SNV · stop gained
Allele type
snv · 1 alt
Cohort
HostSeq (10,487 genomes)
Flags
PASS
Allele frequency
12.4919%
2300 / 18,412 alleles
PASS
Allele count
2300
adjusted · raw: 2305
Allele number
18,412
adjusted · raw: 18,422
Allele frequency
1.25e-01
12.4919% MAF
Homozygotes
167
alt hom carriers
grpmax FAF95
2.43e-01
South Asian · AC=362 AN=1,362
FAF95 max
2.43e-01
South Asian
FAF99 max
2.34e-01
South Asian
Cohort size
10,487
whole genomes
Raw vs adjusted allele counts
ACANAFHom
Adjusted
PASS genotypes only
 230018,412 1.25e-01 167
Raw
all genotypes
 2305 18,422 1.25e-01 —
Allele frequency by ancestry
GRCh38 · HostSeq genomes · Canada
Population AC AN AF Hom
African/African American
afr
 234 1,020
22.9412%
 30
Latino/Admixed American
amr
 81 838
9.6659%
 3
Ashkenazi Jewish
asj
 121 830
14.5783%
 14
East Asian
eas
 138 1,338
10.3139%
 11
European (Finnish)
fin
 0 8 — 0
Middle Eastern
mid
 24 144
16.6667%
 0
European (non-Finnish)
nfe
 1160 11,738
9.8824%
 58
Remaining individuals
oth
 180 1,134
15.8730%
 11
South Asiangrpmax
sas
 362 1,362
26.5786%
 40
Total
 2300 18,412
12.4919%
 167
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 = 2.43e-01.
Filtering allele frequency (FAF)
PopulationFAF 95%FAF 99%
Overall
 1.21e-01 1.19e-01
African/African American
afr
 2.05e-01 1.96e-01
Latino/Admixed American
amr
 7.97e-02 7.34e-02
East Asian
eas
 8.91e-02 8.38e-02
European (non-Finnish)
nfe
 9.41e-02 9.22e-02
South Asian
sas
 2.43e-01 2.34e-01
Sex-stratified allele counts are based on inferred chromosomal sex (XX / XY) from coverage of sex chromosomes in the HostSeq cohort.
XX genotypes
1281 / 10,590  ·  12.0963%
PopulationACANAFHom
African/African American
afr
 132 552 23.913% 18
Latino/Admixed American
amr
 49 456 10.746% 1
Ashkenazi Jewish
asj
 59 420 14.048% 8
East Asian
eas
 77 746 10.322% 7
European (Finnish)
fin
 0 8 — 0
Middle Eastern
mid
 14 68 20.588% 0
European (non-Finnish)
nfe
 684 7,106 9.626% 28
Remaining individuals
oth
 98 608 16.118% 7
South Asian
sas
 168 626 26.837% 15
XY genotypes
1019 / 7,822  ·  13.0274%
PopulationACANAFHom
African/African American
afr
 102 468 21.795% 12
Latino/Admixed American
amr
 32 382 8.377% 2
Ashkenazi Jewish
asj
 62 410 15.122% 6
East Asian
eas
 61 592 10.304% 4
European (Finnish)
fin
 0 — — 0
Middle Eastern
mid
 10 76 13.158% 0
European (non-Finnish)
nfe
 476 4,632 10.276% 30
Remaining individuals
oth
 82 526 15.589% 4
South Asian
sas
 194 736 26.359% 25
Variant quality scores
MQ
Mapping quality
249.8395
FS
Fisher strand bias · lower = better
0.0
MQRankSum
MQ rank sum test
0.0
SOR
Strand odds ratio
0.7258
ReadPosRankSum
Read position rank sum
-0.044
AS_pab_max
Max posterior allele balance
1.0
RF
Random forest score
0.9423
InbreedingCoeff
Inbreeding coefficient
0.0246
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
 26467 23465
Alternate
 32079 27540
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: 370 Carriers above age 80: 120
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)
18,412
Alt allele count
2300
Homozygotes
167
Cross-reference links
gnomAD v4.1 (global) gnomad.broadinstitute.org
gnomAD v2.1 (exome) gnomad.broadinstitute.org
ClinVar — NM_001276270.2:c.1395C>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