1-11981920-G-GTTTTGTTTTT
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_014874.4(MFN2):c.-149-46_-149-45insGTTTTTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★). There are indicators that this mutation may affect the branch point..
Frequency
Genomes: 𝑓 0.0031 ( 4 hom., cov: 0)
Consequence
MFN2
NM_014874.4 intron
NM_014874.4 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.194
Genes affected
MFN2 (HGNC:16877): (mitofusin 2) This gene encodes a mitochondrial membrane protein that participates in mitochondrial fusion and contributes to the maintenance and operation of the mitochondrial network. This protein is involved in the regulation of vascular smooth muscle cell proliferation, and it may play a role in the pathophysiology of obesity. Mutations in this gene cause Charcot-Marie-Tooth disease type 2A2, and hereditary motor and sensory neuropathy VI, which are both disorders of the peripheral nervous system. Defects in this gene have also been associated with early-onset stroke. Two transcript variants encoding the same protein have been identified. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
Variant 1-11981920-G-GTTTTGTTTTT is Benign according to our data. Variant chr1-11981920-G-GTTTTGTTTTT is described in ClinVar as [Likely_benign]. Clinvar id is 1691171.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00307 (423/138008) while in subpopulation AFR AF= 0.0112 (398/35610). AF 95% confidence interval is 0.0103. There are 4 homozygotes in gnomad4. There are 198 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 4 SD gene
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00307 AC: 423AN: 138002Hom.: 4 Cov.: 0
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GnomAD4 genome AF: 0.00307 AC: 423AN: 138008Hom.: 4 Cov.: 0 AF XY: 0.00299 AC XY: 198AN XY: 66270
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 01, 2021 | See Variant Classification Assertion Criteria. - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
BranchPoint Hunter
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at