1-12001454-C-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_014874.4(MFN2):c.870C>T(p.Gly290Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000731 in 1,613,776 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_014874.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 152176Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000758 AC: 19AN: 250626Hom.: 1 AF XY: 0.0000812 AC XY: 11AN XY: 135546
GnomAD4 exome AF: 0.0000677 AC: 99AN: 1461600Hom.: 0 Cov.: 32 AF XY: 0.0000729 AC XY: 53AN XY: 727096
GnomAD4 genome AF: 0.000125 AC: 19AN: 152176Hom.: 0 Cov.: 33 AF XY: 0.000108 AC XY: 8AN XY: 74344
ClinVar
Submissions by phenotype
not provided Benign:4
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MFN2: BP4, BP7 -
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Charcot-Marie-Tooth disease Benign:1
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not specified Benign:1
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. -
MFN2-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Inborn genetic diseases Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Charcot-Marie-Tooth disease type 2 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at