rs12759827
Positions:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000254.3(MTR):c.409+113A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.218 in 860,214 control chromosomes in the GnomAD database, including 24,180 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.18 ( 3384 hom., cov: 32)
Exomes 𝑓: 0.23 ( 20796 hom. )
Consequence
MTR
NM_000254.3 intron
NM_000254.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.550
Genes affected
MTR (HGNC:7468): (5-methyltetrahydrofolate-homocysteine methyltransferase) This gene encodes the 5-methyltetrahydrofolate-homocysteine methyltransferase. This enzyme, also known as cobalamin-dependent methionine synthase, catalyzes the final step in methionine biosynthesis. Mutations in MTR have been identified as the underlying cause of methylcobalamin deficiency complementation group G. Alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, May 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
?
Variant 1-236808886-A-G is Benign according to our data. Variant chr1-236808886-A-G is described in ClinVar as [Benign]. Clinvar id is 1232929.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.266 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MTR | NM_000254.3 | c.409+113A>G | intron_variant | ENST00000366577.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MTR | ENST00000366577.10 | c.409+113A>G | intron_variant | 1 | NM_000254.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.183 AC: 27790AN: 152044Hom.: 3384 Cov.: 32
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GnomAD4 exome AF: 0.226 AC: 159786AN: 708052Hom.: 20796 AF XY: 0.222 AC XY: 83650AN XY: 377180
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GnomAD4 genome ? AF: 0.183 AC: 27784AN: 152162Hom.: 3384 Cov.: 32 AF XY: 0.176 AC XY: 13098AN XY: 74410
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 29, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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