Genetic Variant MTHFR:c.*4074_*4077delAAAA (chr1-11786602-ATTTT-A) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is The variant received -8 classification points (ACMG Germline Pathogenicity v2019). BA1

The NM_005957.5(MTHFR):c.*4074_*4077delAAAA variant causes a 3 prime UTR change. Note: allele frequency estimates from gnomAD may be inaccurate for this variant type (MNP or indel longer than 3 bp) due to technology limitations. The variant allele was found at a cumulative frequency of 0.541 (AC=76,884) in the gnomAD database across 142,024 control chromosomes, including 21,334 homozygotes. The grpmax filtering allele frequency (95% CI) is 0.738. Splicing prediction tools (SpliceAI) predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.54 ( 21334 hom., cov: 0)

Exomes 𝑓: 0.25 ( 0 hom. )

Consequence

MTHFR
NM_005957.5 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.308

Publications

3 publications found

Variant links:

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]

MTHFR Gene-Disease associations (from GenCC):

homocystinuria due to methylene tetrahydrofolate reductase deficiency
Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Natera, PanelApp Australia, Orphanet, G2P, ClinGen, Labcorp Genetics (formerly Invitae)

MTHFR links:

C1orf167 (HGNC:25262): (chromosome 1 open reading frame 167) Implicated in coronary artery disease and stroke. [provided by Alliance of Genome Resources, Jun 2026]

C1orf167 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NM_005957.5, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

Classification according to ACMG Germline Pathogenicity v2019

Classification was made for transcript:

Our verdict: Benign. The variant received -8 points.

Show applied only (1)

Apply	Criterion Code & Title / Strength	Strength	Rationale / Clinical Context
	BA1Stand-alone benign allele frequency (>5%)		GnomAD effective popmax AF >5% — BA1 stand-alone benign; GnomAD reliable popmax AF = 0.7376 — exceeds 5%% threshold (BA1 applied)

Variant Effect in Transcripts

Automated classification analysis was done for transcript: NM_005957.5. You can select a different transcript below to see updated classification assignments.

RefSeq Transcripts

Gene / Transcript	Tags	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
MTHFR NM_005957.5	MANE Select	c.4074_4077delAAAA	3_prime_UTR	Exon 12 of 12	Prot: NP_005948.3
C1orf167 NM_001010881.2	MANE Select	c.3568-770_3568-767delTTTT	intron	Intron 16 of 20	Prot: NP_001010881.1 UniProt: Q5SNV9-1
MTHFR NM_001330358.2		c.4074_4077delAAAA	3_prime_UTR	Exon 12 of 12	Prot: NP_001317287.1 UniProt: P42898-2

MTHFR NM_005957.5

MANE Select

HGVSc / HGVSpc.*4074_*4077delAAAA

Exon rankExon 12 of 12

3_prime_UTR

Prot: NP_005948.3

C1orf167 NM_001010881.2

MANE Select

HGVSc / HGVSpc.3568-770_3568-767delTTTT

Exon rankIntron 16 of 20

intron

Prot: NP_001010881.1UniProt: Q5SNV9-1

MTHFR NM_001330358.2

HGVSc / HGVSpc.*4074_*4077delAAAA

Exon rankExon 12 of 12

3_prime_UTR

Prot: NP_001317287.1UniProt: P42898-2

Ensembl Transcripts

Gene / Transcript	Tags	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
MTHFR ENST00000376590.9	TSL:1MANE Select	c.4074_4077delAAAA	3_prime_UTR	Exon 12 of 12	Prot: ENSP00000365775.3 UniProt: P42898-1
MTHFR ENST00000376592.6	TSL:1	c.4074_4077delAAAA	3_prime_UTR	Exon 12 of 12	Prot: ENSP00000365777.1 UniProt: P42898-1
C1orf167 ENST00000688073.1	MANE Select	c.3568-770_3568-767delTTTT	intron	Intron 16 of 20	Prot: ENSP00000510540.1 UniProt: Q5SNV9-1

MTHFR ENST00000376590.9

TSL:1MANE Select

HGVSc / HGVSpc.*4074_*4077delAAAA

Exon rankExon 12 of 12

3_prime_UTR

Prot: ENSP00000365775.3UniProt: P42898-1

MTHFR ENST00000376592.6

TSL:1

HGVSc / HGVSpc.*4074_*4077delAAAA

Exon rankExon 12 of 12

3_prime_UTR

Prot: ENSP00000365777.1UniProt: P42898-1

C1orf167 ENST00000688073.1

MANE Select

HGVSc / HGVSpc.3568-770_3568-767delTTTT

Exon rankIntron 16 of 20

intron

Prot: ENSP00000510540.1UniProt: Q5SNV9-1

Frequencies

Allele frequencies (AF), counts (AC/AN), homozygotes and coverage

Common (AF > 0.05 / Hom > 5)

Rare (AF ≤ 0.0001 / Hom ≤ 1)

Source / population	AF	AC	Hom	AN	Coverage
Global population databases 5 sources Large-scale international reference populations
GnomAD3 genomes	AF: 0.542	AC:76895	Hom:21344	AN:141988	Cov:0
GnomAD4 exome	AF: 0.250	AC:1	Hom:0	AN:4	Cov:
GnomAD4 genome	AF: 0.541	AC:76883	Hom:21334	AN:142020	Cov:0
TOPMed (Bravo) Warning	AF: 0.660	AC:174693	Hom:65581	AN:264690	Cov:
ALFA (dbGaP/dbSNP Allele Frequency Aggregator)	AF: 0.438	AC:2368	Hom:600	AN:5410	Cov:
Local & regional cohorts 3 sources Population-specific and national genomic databases
ABraOM SABE-WGS-1171	AF: 0.692	AC:763	Hom:248	AN:1102	Cov:
Turkish Variome	AF: 0.475	AC:616	Hom:150	AN:1296	Cov:
UK10K	AF: 0.793	AC:5994	Hom:	AN:7562	Cov:

Showing 8 sources

ClinVar

Not reported in ClinVar

Computational Scores

Algorithm	Calibrated pred.	Score	Prediction
Mutation Taster	N/A	100/0	polymorphism (auto)
PhyloP100	Benign	0.31

Showing 2 of 2 scores

Splicing Scores

Algorithm	Calibrated pred.	Score	Prediction
SpliceAI score (max)	Benign	0.0	Details are displayed if max score is > 0.2

Showing 1 of 1 scores

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

MaveDB functional evidence

MaveDB is a public repository of laboratory assays that test the effect of thousands of variants at once — treat this as supporting research data and interpret it with great caution; it is not a clinical classification.

No MaveDB functional evidence found for this variant.

Publications

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1-11786602-ATTTTTTTTT-ATTTTT

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

Classification according to ACMG Germline Pathogenicity v2019

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational Scores

Splicing Scores

MaveDB functional evidence

Publications

Other links and lift over

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

Classification according to ACMG Germline Pathogenicity v2019

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational Scores

Splicing Scores

MaveDB functional evidence ?

Publications

Other links and lift over

MaveDB functional evidence