2-201078937-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_002491.3(NDUFB3):āc.55T>Gā(p.Tyr19Asp) variant causes a missense change. The variant allele was found at a frequency of 0.0000198 in 1,613,160 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NDUFB3 | NM_002491.3 | c.55T>G | p.Tyr19Asp | missense_variant | Exon 2 of 3 | ENST00000237889.9 | NP_002482.1 | |
NDUFB3 | NM_001257102.2 | c.55T>G | p.Tyr19Asp | missense_variant | Exon 3 of 4 | NP_001244031.1 | ||
NDUFB3 | XM_011511230.4 | c.55T>G | p.Tyr19Asp | missense_variant | Exon 3 of 4 | XP_011509532.1 | ||
NDUFB3 | XM_047444488.1 | c.55T>G | p.Tyr19Asp | missense_variant | Exon 3 of 4 | XP_047300444.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152192Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 250976Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135618
GnomAD4 exome AF: 0.0000212 AC: 31AN: 1460968Hom.: 0 Cov.: 30 AF XY: 0.0000138 AC XY: 10AN XY: 726810
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152192Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74356
ClinVar
Submissions by phenotype
not provided Uncertain:1
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: "Deleterious"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C15"). 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. This sequence change replaces tyrosine, which is neutral and polar, with aspartic acid, which is acidic and polar, at codon 19 of the NDUFB3 protein (p.Tyr19Asp). This variant is present in population databases (rs772160306, gnomAD 0.002%). This variant has not been reported in the literature in individuals affected with NDUFB3-related conditions. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at