rs17284990
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_006441.4(MTHFS):c.380-6413A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.184 in 152,128 control chromosomes in the GnomAD database, including 3,046 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.18 ( 3046 hom., cov: 32)
Consequence
MTHFS
NM_006441.4 intron
NM_006441.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.280
Genes affected
MTHFS (HGNC:7437): (methenyltetrahydrofolate synthetase) The protein encoded by this gene is an enzyme that catalyzes the conversion of 5-formyltetrahydrofolate to 5,10-methenyltetrahydrofolate, a precursor of reduced folates involved in 1-carbon metabolism. An increased activity of the encoded protein can result in an increased folate turnover rate and folate depletion. Three transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Jun 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MTHFS | NM_006441.4 | c.380-6413A>G | intron_variant | ENST00000258874.4 | |||
ST20-MTHFS | NM_001199760.2 | c.308-6413A>G | intron_variant | ||||
MTHFS | NM_001199758.1 | c.209-6413A>G | intron_variant | ||||
MTHFS | NR_037654.2 | n.487-6413A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MTHFS | ENST00000258874.4 | c.380-6413A>G | intron_variant | 1 | NM_006441.4 | P1 | |||
MTHFS | ENST00000559722.2 | c.467-6413A>G | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.184 AC: 27991AN: 152010Hom.: 3047 Cov.: 32
GnomAD3 genomes
?
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152010
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.184 AC: 27983AN: 152128Hom.: 3046 Cov.: 32 AF XY: 0.185 AC XY: 13766AN XY: 74366
GnomAD4 genome
?
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27983
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152128
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32
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13766
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74366
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573
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at