1:11796321-G>A

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 3P and 12B. PM1 PP3 BP4_Strong BA1

The NM_005957.5(MTHFR):c.665C>T(p.Ala222Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.318 in 1,613,846 control chromosomes in the GnomAD database, including 87,723 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as drug response (★★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin ClinVar. Synonymous variant affecting the same amino acid position (i.e. A222A) has been classified as Likely benign.

• Frequency:
  • Genomes: 𝑓 0.28 (6918 hom., cov: 32)
  • Exomes 𝑓: 0.32 (80805 hom.)
• Consequence: MTHFR NM_005957.5 missense
• Clinical Significance: drug response reviewed by expert panel P:3 U:6 B:9 O:3
• Conservation: PhyloP100: 9.14

Genes affected

MTHFR (HGNC:7436): (methylenetetrahydrofolate reductase) The protein encoded by this gene catalyzes the conversion of 5,10-methylenetetrahydrofolate to 5-methyltetrahydrofolate, a co-substrate for homocysteine remethylation to methionine. Genetic variation in this gene influences susceptibility to occlusive vascular disease, neural tube defects, colon cancer and acute leukemia, and mutations in this gene are associated with methylenetetrahydrofolate reductase deficiency.[provided by RefSeq, Oct 2009]

ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

• PM1: In a hotspot region, there are 2 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 4 uncertain in NM_005957.5
• PP3: Multiple lines of computational evidence support a deleterious effect 8: AlphaMissense, BayesDel_noAF, Cadd, Dann, Eigen, MutationAssessor, phyloP100way_vertebrate, REVEL [when FATHMM_MKL, MetaRNN, MutationTaster was below the threshold]
• BP4: Computational evidence support a benign effect (MetaRNN=0.0016527474).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.435 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MTHFR	NM_005957.5	c.665C>T	p.Ala222Val	missense_variant	5/12	ENST00000376590.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MTHFR	ENST00000376590.9	c.665C>T	p.Ala222Val	missense_variant	5/12	1	NM_005957.5	A1

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41856 AN: 151970 Hom.: 6918 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.484

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.461

Gnomad EAS AF: 0.302

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.300

GnomAD3 exomes AF: 0.315 AC: 79177 AN: 251468 Hom.: 14637 AF XY: 0.309 AC XY: 41934 AN XY: 135906

Gnomad AFR exome AF: 0.108

Gnomad AMR exome AF: 0.503

Gnomad ASJ exome AF: 0.457

Gnomad EAS exome AF: 0.290

Gnomad SAS exome AF: 0.145

Gnomad FIN exome AF: 0.231

Gnomad NFE exome AF: 0.340

Gnomad OTH exome AF: 0.330

GnomAD4 exome AF: 0.323 AC: 471698 AN: 1461758 Hom.: 80805 Cov.: 40 AF XY: 0.318 AC XY: 231451 AN XY: 727162

Gnomad4 AFR exome AF: 0.106

Gnomad4 AMR exome AF: 0.489

Gnomad4 ASJ exome AF: 0.460

Gnomad4 EAS exome AF: 0.355

Gnomad4 SAS exome AF: 0.149

Gnomad4 FIN exome AF: 0.233

Gnomad4 NFE exome AF: 0.337

Gnomad4 OTH exome AF: 0.308

GnomAD4 genome AF: 0.275 AC: 41850 AN: 152088 Hom.: 6918 Cov.: 32 AF XY: 0.273 AC XY: 20316 AN XY: 74360

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.444

Gnomad4 ASJ AF: 0.461

Gnomad4 EAS AF: 0.302

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.235

Gnomad4 NFE AF: 0.337

Gnomad4 OTH AF: 0.298

Alfa AF: 0.337 Hom.: 23149

Bravo AF: 0.291

TwinsUK AF: 0.330 AC: 1224

ALSPAC AF: 0.334 AC: 1288

ESP6500AA AF: 0.122 AC: 536

ESP6500EA AF: 0.347 AC: 2983

ExAC AF: 0.304 AC: 36865

Asia WGS AF: 0.190 AC: 662 AN: 3478

ClinVar

Significance: drug response

Submissions summary: Pathogenic:3Uncertain:6Benign:9Other:3

Revision: reviewed by expert panel

LINK:

Submissions by phenotype

Homocystinuria due to methylene tetrahydrofolate reductase deficiency Pathogenic:2Uncertain:1Benign:2

Benign, no assertion criteria provided	clinical testing	Natera, Inc.	Dec 07, 2019	- -
Benign, criteria provided, single submitter	clinical testing	Invitae	Feb 01, 2024	- -
Pathogenic, criteria provided, single submitter	clinical testing	Myriad Genetics, Inc.	Dec 16, 2019	NM_005957.4(MTHFR):c.665C>T(A222V) is a common variant present in approximately 30% of the general population. While many individuals who are homozygous for this variant are asymptomatic, some may have mild MTHFR deficiency associated with increased plasma homocysteine. Sources cited for classification include the following: PMID 7647779, 8837319, 9545406, 11781870, 12560871, 8903338, 9789068, 11929966, 15565101, 17436239, 12356947, 9133512, 12196644 and 9798595. Classification of NM_005957.4(MTHFR):c.665C>T(A222V) is based on the following criteria: This is a well-established variant in the literature that has been observed more frequently in patients with mild MTHFR deficiency than in healthy populations and there is functional data showing deficient protein function. Please note: this variant was assessed in the context of healthy population screening. -
Uncertain significance, no assertion criteria provided	research	Neurology Department, Peking University First Hospital	Apr 23, 2020	- -
Pathogenic, criteria provided, single submitter	clinical testing	Centre for Mendelian Genomics, University Medical Centre Ljubljana	Jan 17, 2019	This variant was classified as: Pathogenic. The following ACMG criteria were applied in classifying this variant: No criteria apply. This variant was detected in homozygous state. -

not specified Benign:4

Benign, criteria provided, single submitter	clinical testing	GeneDx	Apr 25, 2016	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Benign, no assertion criteria provided	clinical testing	Clinical Genetics, Academic Medical Center	-	- -
Benign, no assertion criteria provided	clinical testing	Department of Pathology and Laboratory Medicine, Sinai Health System	-	- -
Benign, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	-	- -

not provided Uncertain:2Other:1

Uncertain significance, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Nov 29, 2023	The MTHFR c.665C>T; p.Ala222Val variant (rs1801133), also known as C677T or the thermolabile variant, is listed in the ClinVar database (Variation ID: 3520) and is observed in the general population with an overall allele frequency of 30.8% (87,234/282,784 alleles including 15,819 homozygotes) in the Genome Aggregation Database. The thermolabile c.665C>T variant in the homozygous state has been correlated with reduced enzyme activity and increased homocysteine (Frosst 1995). The practice guidelines from The American College of Medical Genetics state that this variant in the heterozygous state is unlikely to be of clinical significance (Hickey 2013); however, a possible effect of this variant when paired with a pathogenic MTHFR variant on the opposite chromosome cannot be excluded. Additionally, the practice guidelines state that an individual who is homozygous for the c.665C>T; p.Ala222Val variant and has elevated homocysteine may be at mildly increased risk for venous thromboembolism and recurrent pregnancy loss (Hickey 2013). The variant is considered a ''susceptibility'' or an ''association'' variant. REFERENCES Frosst P et al. A candidate genetic risk factor for vascular disease: a common mutation in methylenetetrahydrofolate reductase. Nat Genet. 1995 May;10(1):111-3. PMID: 7647779. Hickey SE et al. ACMG Practice Guideline: lack of evidence for MTHFR polymorphism testing. Genet Med. 2013 Feb;15(2):153-6. PMID: 23288205. -
Uncertain significance, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Jan 01, 2024	MTHFR: PM3, PM2:Supporting -
other, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Jan 13, 2017	- Variant classified as "other reportable" ??? variant is clinically benign (not associated with disease) but is reported when observed (e.g. pseudodeficiency alleles).

MTHFR THERMOLABILE POLYMORPHISM Pathogenic:1Benign:1

Pathogenic, no assertion criteria provided	clinical testing	FirmaLab, FirmaLab	-	- -
Benign, no assertion criteria provided	literature only	OMIM	Sep 29, 2023	- -

Neural tube defects, folate-sensitive Benign:2

Likely benign, criteria provided, single submitter	clinical testing	Mendelics	May 28, 2019	- -
Likely benign, no assertion criteria provided	reference population	iDNA Genomics	-	- -

Stroke disorder Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Institute of Human Genetics, University Hospital Muenster

Jan 06, 2022

ACMG categories: PS3,PS4,PM1,BA1 -

Gastrointestinal stromal tumor Uncertain:1

Uncertain significance, no assertion criteria provided

case-control

Department of Pharmacy and Biotechnology, University of Bologna

-

- -

Thrombophilia due to thrombin defect Uncertain:1

Uncertain significance, no assertion criteria provided

curation

Department Of Genetics, Sultan Qaboos University Hospital, Sultan Qaboos University

Dec 30, 2017

- -

methotrexate response - Toxicity Other:1

drug response, reviewed by expert panel

curation

PharmGKB

Mar 24, 2021

PharmGKB Level of Evidence 2A: Variants in Level 2A clinical annotations are found in PharmGKB’s Tier 1 Very Important Pharmacogenes (VIPs). These variants are in known pharmacogenes, implying causation of drug phenotype is more likely. These clinical annotations describe variant-drug combinations with a moderate level of evidence supporting the association. For example, the association may be found in multiple cohorts, but there may be a minority of studies that do not support the majority assertion. Level 2A clinical annotations must be supported by at least two independent publications. Drug-variant association: Toxicity

Neoplasm of stomach Other:1

not provided, no classification provided

literature only

Database of Curated Mutations (DoCM)

Mar 10, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.63

BayesDel_addAF

Uncertain

0.12

D

BayesDel_noAF

Pathogenic

0.55

Cadd

Pathogenic

28

Dann

Pathogenic

1.0

DEOGEN2

Pathogenic

0.94

D;.;.;D;.;.;.

Eigen

Pathogenic

0.74

Eigen_PC

Uncertain

0.66

FATHMM_MKL

Pathogenic

0.98

D

MetaRNN

Benign

0.0017

T;T;T;T;T;T;T

MetaSVM

Benign

-1.5

T

MutationAssessor

Pathogenic

3.0

M;.;.;M;.;.;.

MutationTaster

Benign

8.6e-8

P;P;P;P

PrimateAI

Uncertain

0.62

T

PROVEAN

Uncertain

-3.8

D;D;D;D;.;.;.

REVEL

Pathogenic

0.84

Sift

Uncertain

0.0020

D;D;D;D;.;.;.

Sift4G

Uncertain

0.053

T;D;D;T;.;.;.

Polyphen

1.0

D;.;.;D;.;.;.

Vest4

0.47

MPC

0.93

ClinPred

0.020

T

GERP RS

5.1

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.83

gMVP

0.94

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1801133; hg19: chr1-11856378; COSMIC: COSV64876755; COSMIC: COSV64876755;