2-201078985-A-C
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_002491.3(NDUFB3):āc.103A>Cā(p.Lys35Gln) variant causes a missense change. The variant allele was found at a frequency of 0.000044 in 1,613,262 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_002491.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NDUFB3 | NM_002491.3 | c.103A>C | p.Lys35Gln | missense_variant | Exon 2 of 3 | ENST00000237889.9 | NP_002482.1 | |
NDUFB3 | NM_001257102.2 | c.103A>C | p.Lys35Gln | missense_variant | Exon 3 of 4 | NP_001244031.1 | ||
NDUFB3 | XM_011511230.4 | c.103A>C | p.Lys35Gln | missense_variant | Exon 3 of 4 | XP_011509532.1 | ||
NDUFB3 | XM_047444488.1 | c.103A>C | p.Lys35Gln | missense_variant | Exon 3 of 4 | XP_047300444.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152224Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000480 AC: 12AN: 249826Hom.: 0 AF XY: 0.0000592 AC XY: 8AN XY: 135076
GnomAD4 exome AF: 0.0000472 AC: 69AN: 1461038Hom.: 0 Cov.: 31 AF XY: 0.0000495 AC XY: 36AN XY: 726820
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152224Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74372
ClinVar
Submissions by phenotype
not provided Uncertain:1
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. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals affected with NDUFB3-related conditions. This variant is present in population databases (rs768388896, gnomAD 0.01%). This sequence change replaces lysine, which is basic and polar, with glutamine, which is neutral and polar, at codon 35 of the NDUFB3 protein (p.Lys35Gln). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at