Variant classification summary

NM_005957.5:c.665C>T

MTHFR · NP_005948.3:p.(Ala222Val) · NM_005957.5

GRCh37: chr1:11856378 G>A · GRCh38: chr1:11796321 G>A

Gene: MTHFR Transcript: NM_005957.5

Final call

Benign

PS3 supporting PP3 moderate BA1 stand-alone benign BS1 strong

Variant details

Gene

MTHFR

Transcript

NM_005957.5

Protein

NP_005948.3:p.(Ala222Val)

gnomAD AF

0.3182137576943525 (v4.1)

ClinVar

drug response

OncoKB

Unknown Oncogenic Effect

Classification rationale

Interpretation summary

Generated evidence synthesis

1

Benign: BA1 is met because gnomAD allele frequency is 0.318214, exceeding the 0.05 stand-alone threshold.

2

Benign: BS1 is met at strong strength because the high allele frequency and 87,723 homozygotes are incompatible with a rare fully penetrant disorder.

3

Supporting pathogenic evidence: PS3 shows reduced p.Ala222Val enzyme activity and increased thermolability, but no pathogenic combination is satisfied.

4

Moderate pathogenic evidence: PP3 is met by REVEL 0.842, but it does not satisfy a pathogenic combination with PS3.

Final determination: Under the generic ACMG/AMP 2015 fallback, BA1 alone is sufficient for a Benign classification; BS1 is additionally met, and no pathogenic combination is satisfied.

Criteria assessment

ACMG/AMP criteria review

Criteria shown when status is available

All criteria require review: For research and educational purposes only.

Criterion	Status	Rationale	Evidence used
PVS1	N/A	Not applicable: PVS1 requires a null variant (nonsense, frameshift, canonical splice, start-loss or stop-loss), and this is a missense variant.	pvs1_generic_framework generic_acmg_combination_rules
PS1	Not met	Not met: no previously established pathogenic variant with the same Ala222Val amino-acid change from a different nucleotide change was identified.	PMID:12673793 PMID:7647779 clinvar
PS2	Not assessed	Not assessed: no proband phenotype, confirmed maternity and paternity, de novo genotype, or family-history information is documented.
PS3	Met	Met at supporting: p.Ala222Val showed approximately 30% homozygous enzyme activity and increased thermolability across expression and patient-fibroblast assays.	PMID:7647779 PMID:12673793 PMID:25736335 PMID:26872964
PS4	Not assessed	Not assessed: no verifiable exact-variant affected-versus-control counts or odds ratio with a 95% confidence interval are available for the PS4 >5.0 and CI-excluding-1 requirement.	gnomad_v4
PM1	Not met	Not met: although A222V lies in the catalytic domain, gnomAD v4.1 reports AF 0.318214 with 87,723 homozygotes, demonstrating common benign variation.	PMID:12673793 gnomad_v4
PM2	Not met	Not met: gnomAD AF is 0.318214, vastly above the generic PM2 supporting threshold of 0.0001 or less.	gnomad_v2 gnomad_v4 PMID:25741868
PM3	Not assessed	Not assessed: no affected-proband observation identifies a pathogenic partner in trans or provides parental/offspring phase testing.
PM4	N/A	Not applicable: PM4 requires a protein-length change, and this is a missense variant.	pvs1_generic_framework generic_acmg_combination_rules
PM5	Not met	Not met: no different missense substitution at MTHFR residue Ala222 with an established pathogenic classification was identified.	pm5_candidates PMID:12673793 PMID:26872964
PM6	Not assessed	Not assessed: no affected proband with an assumed de novo variant and documented parental-testing or family-history status is provided.
PP1	Not assessed	Not assessed: zero affected relatives, informative meioses, or familial genotype–phenotype segregation observations are documented.
PP2	Not met	Not met: gnomAD v4.1 shows A222V at AF 0.318214 with 87,723 homozygotes, incompatible with a low rate of benign missense variation.	gnomad_v4 PMID:26872964
PP3	Met	Met at moderate strength: missense REVEL score 0.842 meets the generic PP3 threshold of >=0.773 but is below the >=0.932 strong threshold.	revel
PP4	Not assessed	Not assessed: no patient phenotype or family history is documented to evaluate specificity for a single-gene disease.
PP5	Not met	Not met: the exact-variant ClinVar expert-panel classification is drug response, not Pathogenic or Likely pathogenic.	clinvar
BA1	Met	Met: gnomAD allele frequency is 0.318214, far above the generic BA1 stand-alone threshold of 0.05.	gnomad_v2 gnomad_v4 PMID:25741868
BS1	Met	Met: AF 0.318214 with 87,723 homozygotes is far above the generic BS1 default threshold of 0.01 and incompatible with a rare fully penetrant disorder.	gnomad_v2 gnomad_v4 PMID:25741868
BS2	Not assessed	Not assessed: 87,723 homozygotes are reported, but healthy-adult status and early full penetrance are not established.	gnomad_v2 gnomad_v4 PMID:25741868
BS3	Not met	Not met: functional studies report approximately 30% homozygous activity and 21% heat-treated residual activity, indicating impairment rather than no damaging effect.	PMID:7647779 PMID:25736335
BS4	Not assessed	Not assessed: no affected relatives with tested negative genotypes or phenotype-reviewed non-segregation observations are documented.
BP1	Not met	Not met: MTHFR deficiency literature includes multiple missense mutations, so disease is not shown to be caused primarily by truncating variants.	PMID:10679944 PMID:26872964
BP2	Not assessed	Not assessed: no pathogenic allelic partner is documented with the required cis or trans phase for BP2.
BP3	N/A	Not applicable: BP3 requires an in-frame indel in a repeat region, and this is a missense variant.	pvs1_generic_framework generic_acmg_combination_rules
BP4	Not met	Not met: missense REVEL score 0.842 exceeds the generic BP4 supporting threshold of <=0.29, so the result is outside the benign range.	revel
BP5	Not assessed	Not assessed: no case-level alternate molecular diagnosis is documented for a patient carrying this variant.
BP6	Not met	Not met: the exact-variant ClinVar expert-panel classification is drug response, not Benign or Likely benign.	clinvar
BP7	N/A	Not applicable: BP7 requires a synonymous variant, and this is a missense variant.	generic_acmg_combination_rules

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