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 / MTHFR c.665C>T / gnomAD Canada
gnomAD Canada v1.0 · HostSeq
NM_005957.5:c.665C>T
NP_005948.3:p.(Ala222Val)  ·  MTHFR
GRCh38
chr1:11,796,321 G>A
GRCh37
chr1:11856378 G>A
rsID
rs1801133
Type
SNV · missense variant
Allele type
snv · 1 alt
Cohort
HostSeq (10,487 genomes)
Flags
PASS
Allele frequency
32.0194%
5889 / 18,392 alleles
PASS
Allele count
5889
adjusted · raw: 5909
Allele number
18,392
adjusted · raw: 18,422
Allele frequency
3.20e-01
32.0194% MAF
Homozygotes
1086
alt hom carriers
grpmax FAF95
3.89e-01
Latino/Admixed American · AC=356 AN=836
FAF95 max
3.89e-01
Latino/Admixed American
FAF99 max
3.75e-01
Latino/Admixed American
Cohort size
10,487
whole genomes
Raw vs adjusted allele counts
ACANAFHom
Adjusted
PASS genotypes only
 588918,392 3.20e-01 1086
Raw
all genotypes
 5909 18,422 3.21e-01 —
Allele frequency by ancestry
GRCh38 · HostSeq genomes · Canada
Population AC AN AF Hom
African/African American
afr
 86 1,020
8.4314%
 2
Latino/Admixed Americangrpmax
amr
 356 836
42.5837%
 84
Ashkenazi Jewish
asj
 377 830
45.4217%
 95
East Asian
eas
 302 1,338
22.5710%
 45
European (Finnish)
fin
 3 8
37.5000%
 0
Middle Eastern
mid
 50 144
34.7222%
 6
European (non-Finnish)
nfe
 4153 11,720
35.4352%
 793
Remaining individuals
oth
 335 1,136
29.4894%
 44
South Asian
sas
 227 1,360
16.6912%
 17
Total
 5889 18,392
32.0194%
 1086
Population codes are displayed as sourced from gnomAD Canada v1.0 without relabelling. Bar widths scaled relative to the grpmax population (Latino/Admixed American). Grpmax FAF95 = 3.89e-01.
Filtering allele frequency (FAF)
PopulationFAF 95%FAF 99%
Overall
 3.13e-01 3.11e-01
African/African American
afr
 6.99e-02 6.46e-02
Latino/Admixed American
amr
 3.89e-01 3.75e-01
East Asian
eas
 2.05e-01 1.97e-01
European (non-Finnish)
nfe
 3.45e-01 3.42e-01
South Asian
sas
 1.49e-01 1.42e-01
Sex-stratified allele counts are based on inferred chromosomal sex (XX / XY) from coverage of sex chromosomes in the HostSeq cohort.
XX genotypes
3450 / 10,584  ·  32.5964%
PopulationACANAFHom
African/African American
afr
 45 552 8.152% 1
Latino/Admixed American
amr
 194 456 42.544% 45
Ashkenazi Jewish
asj
 194 420 46.190% 50
East Asian
eas
 170 746 22.788% 25
European (Finnish)
fin
 3 8 37.500% 0
Middle Eastern
mid
 26 68 38.235% 3
European (non-Finnish)
nfe
 2522 7,098 35.531% 482
Remaining individuals
oth
 181 610 29.672% 24
South Asian
sas
 115 626 18.371% 9
XY genotypes
2439 / 7,808  ·  31.2372%
PopulationACANAFHom
African/African American
afr
 41 468 8.761% 1
Latino/Admixed American
amr
 162 380 42.632% 39
Ashkenazi Jewish
asj
 183 410 44.634% 45
East Asian
eas
 132 592 22.297% 20
European (Finnish)
fin
 0 — — 0
Middle Eastern
mid
 24 76 31.579% 3
European (non-Finnish)
nfe
 1631 4,622 35.288% 311
Remaining individuals
oth
 154 526 29.278% 20
South Asian
sas
 112 734 15.259% 8
Variant quality scores
MQ
Mapping quality
249.7733
FS
Fisher strand bias · lower = better
0.0
MQRankSum
MQ rank sum test
0.0
SOR
Strand odds ratio
0.7133
ReadPosRankSum
Read position rank sum
0.04
AS_pab_max
Max posterior allele balance
1.0
RF
Random forest score
0.9423
InbreedingCoeff
Inbreeding coefficient
0.0729
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
 45248 43235
Alternate
 70401 65937
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: 614 Carriers above age 80: 231
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)
18,392
Alt allele count
5889
Homozygotes
1086
Cross-reference links
gnomAD v4.1 (global) gnomad.broadinstitute.org
gnomAD v2.1 (exome) gnomad.broadinstitute.org
ClinVar — NM_005957.5:c.665C>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