rs74052923
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_014874.4(MFN2):c.1039-19G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0081 in 1,614,022 control chromosomes in the GnomAD database, including 818 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_014874.4 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0423 AC: 6438AN: 152028Hom.: 437 Cov.: 33
GnomAD3 exomes AF: 0.0112 AC: 2817AN: 251480Hom.: 170 AF XY: 0.00863 AC XY: 1173AN XY: 135918
GnomAD4 exome AF: 0.00453 AC: 6628AN: 1461876Hom.: 379 Cov.: 33 AF XY: 0.00401 AC XY: 2914AN XY: 727234
GnomAD4 genome AF: 0.0424 AC: 6450AN: 152146Hom.: 439 Cov.: 33 AF XY: 0.0399 AC XY: 2971AN XY: 74390
ClinVar
Submissions by phenotype
not specified Benign:2
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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. -
Charcot-Marie-Tooth disease Benign:1
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Charcot-Marie-Tooth disease type 2 Benign:1
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not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at