Interim display. This page is a temporary, independent display of gnomAD Canada v1.0 data, offered until the gnomAD Canada team releases its own browser; it is not the official source. Data are provided as is, without any warranty of accuracy or completeness, and may contain errors or omissions. Verify results against the official dataset from BCGSC (bcgsc.ca/gnomad) before relying on them. For research and educational use only; not for clinical decision-making. Interim display. Not the official source; data provided as is. Verify against BCGSC.
Home / MSH2 c.942+3A>T / gnomAD Canada
gnomAD Canada v1.0 · HostSeq
NM_000251.3:c.942+3A>T
NP_000242.1:p.?  ·  MSH2
GRCh38
chr2:47,414,421 A>T
GRCh37
chr2:47641560 A>T
rsID
—
Type
MULTI-SNV · splice donor region variant
Allele type
snv · 2 alt
Cohort
HostSeq (10,487 genomes)
Flags
lcr, singleton, was_split, AC0, RF
Allele frequency
Absent
0 / 142 alleles
lcr PASS
Variant not observed in HostSeq
This variant was not observed in the gnomAD Canada v1.0 HostSeq cohort (10,487 genomes, 142 alleles genotyped at this position). An allele count of 0 does not mean the variant is pathogenic — it means it was not seen in this specific Canadian cohort. Consult gnomAD global (v2.1 / v4.1) for broader population data.
Allele count
0
adjusted · raw: 1
Allele number
142
adjusted · raw: 672
Allele frequency
0
0.0000% MAF
Homozygotes
0
alt hom carriers
grpmax FAF95
—
· AC=0 AN=—
FAF95 max
—
—
FAF99 max
—
—
Cohort size
10,487
whole genomes
Raw vs adjusted allele counts
ACANAFHom
Adjusted
PASS genotypes only
 0142 — 0
Raw
all genotypes
 1 672 1.49e-03 —
This variant was not observed in the gnomAD Canada v1.0 HostSeq cohort (AC = 0 across 142 alleles). No per-ancestry frequency breakdown is available.
Sex-stratified data is not available — this variant was not observed in the HostSeq cohort.
Variant quality scores
MQ
Mapping quality
244.6711
FS
Fisher strand bias · lower = better
6.841
MQRankSum
MQ rank sum test
-0.307
SOR
Strand odds ratio
0.3122
ReadPosRankSum
Read position rank sum
0.921
AS_pab_max
Max posterior allele balance
0.146
RF
Random forest score
0.0954
InbreedingCoeff
Inbreeding coefficient
-0.0015
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
 13 28
Alternate
 658 618
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
AC0 RF 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.
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)
142
Alt allele count
0
Homozygotes
0
Cross-reference links
gnomAD v4.1 (global) gnomad.broadinstitute.org
gnomAD v2.1 (exome) gnomad.broadinstitute.org
ClinVar — NM_000251.3:c.942+3A>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