Home / MLH1 c.1039-25T>A / gnomAD Canada
gnomAD Canada v1.0 · HostSeq
NM_000249.4:c.1039-25T>A
NP_000240.1:p.?  ·  MLH1
GRCh38
chr3:37,025,612 T>A
GRCh37
chr3:37067103 T>A
rsID
rs764852270
Type
SNV · intron variant
Allele type
snv · 1 alt
Cohort
HostSeq (10,487 genomes)
Flags
lcr, was_split
Allele frequency
0.0408%
7 / 17,144 alleles
lcr PASS
Allele count
7
adjusted · raw: 9
Allele number
17,144
adjusted · raw: 17,342
Allele frequency
4.08e-04
0.0408% MAF
Homozygotes
0
alt hom carriers
grpmax FAF95
—
African/African American · AC=1 AN=734
FAF95 max
7.35e-05
European (non-Finnish)
FAF99 max
3.88e-05
European (non-Finnish)
Cohort size
10,487
whole genomes
Raw vs adjusted allele counts
ACANAFHom
Adjusted
PASS genotypes only
 717,144 4.08e-04 0
Raw
all genotypes
 9 17,342 5.19e-04 —
Allele frequency by ancestry
GRCh38 · HostSeq genomes · Canada
Population AC AN AF Hom
African/African Americangrpmax
afr
 1 734
0.1362%
 0
Latino/Admixed American
amr
 0 776 — 0
Ashkenazi Jewish
asj
 2 746
0.2681%
 0
East Asian
eas
 0 1,326 — 0
European (Finnish)
fin
 0 8 — 0
Middle Eastern
mid
 1 138
0.7246%
 0
European (non-Finnish)
nfe
 3 11,068
0.0271%
 0
Remaining individuals
oth
 0 1,054 — 0
South Asian
sas
 0 1,294 — 0
Total
 7 17,144
0.0408%
 0
Population codes are displayed as sourced from gnomAD Canada v1.0 without relabelling. Bar widths scaled relative to the grpmax population (African/African American).
Filtering allele frequency (FAF)
PopulationFAF 95%FAF 99%
Overall
 1.91e-04 1.35e-04
European (non-Finnish)
nfe
 7.35e-05 3.88e-05
Sex-stratified allele counts are based on inferred chromosomal sex (XX / XY) from coverage of sex chromosomes in the HostSeq cohort.
XX genotypes
5 / 9,850  ·  0.0508%
PopulationACANAFHom
African/African American
afr
 1 400 0.250% 0
Latino/Admixed American
amr
 0 426 — 0
Ashkenazi Jewish
asj
 1 380 0.263% 0
East Asian
eas
 0 738 — 0
European (Finnish)
fin
 0 8 — 0
Middle Eastern
mid
 0 66 — 0
European (non-Finnish)
nfe
 3 6,680 0.045% 0
Remaining individuals
oth
 0 562 — 0
South Asian
sas
 0 590 — 0
XY genotypes
2 / 7,294  ·  0.0274%
PopulationACANAFHom
African/African American
afr
 0 334 — 0
Latino/Admixed American
amr
 0 350 — 0
Ashkenazi Jewish
asj
 1 366 0.273% 0
East Asian
eas
 0 588 — 0
European (Finnish)
fin
 0 — — 0
Middle Eastern
mid
 1 72 1.389% 0
European (non-Finnish)
nfe
 0 4,388 — 0
Remaining individuals
oth
 0 492 — 0
South Asian
sas
 0 704 — 0
Variant quality scores
MQ
Mapping quality
245.0887
FS
Fisher strand bias · lower = better
2.4233
MQRankSum
MQ rank sum test
0.058
SOR
Strand odds ratio
0.7967
ReadPosRankSum
Read position rank sum
1.361
AS_pab_max
Max posterior allele balance
1.0
RF
Random forest score
0.2244
InbreedingCoeff
Inbreeding coefficient
-0.0005
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
 197 204
Alternate
 194 171
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 above age 80: 1
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)
17,144
Alt allele count
7
Homozygotes
0
Cross-reference links
gnomAD v4.1 (global) gnomad.broadinstitute.org
gnomAD v2.1 (exome) gnomad.broadinstitute.org
ClinVar — NM_000249.4:c.1039-25T>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