X-47142364-A-C
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBP6BS2
The NM_001135998.3(NDUFB11):āc.415T>Gā(p.Ser139Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000413 in 1,209,551 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001135998.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000895 AC: 1AN: 111672Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33836
GnomAD4 exome AF: 0.00000364 AC: 4AN: 1097879Hom.: 0 Cov.: 31 AF XY: 0.00000551 AC XY: 2AN XY: 363255
GnomAD4 genome AF: 0.00000895 AC: 1AN: 111672Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33836
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
NDUFB11: BP4 -
This sequence change replaces serine, which is neutral and polar, with alanine, which is neutral and non-polar, at codon 149 of the NDUFB11 protein (p.Ser149Ala). This variant is present in population databases (rs199837826, gnomAD 0.001%). This variant has not been reported in the literature in individuals affected with NDUFB11-related conditions. ClinVar contains an entry for this variant (Variation ID: 1437660). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at