rs4582532
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001354516.2(NDUFAF6):c.-263-966G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.496 in 151,590 control chromosomes in the GnomAD database, including 18,946 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.50 ( 18946 hom., cov: 31)
Consequence
NDUFAF6
NM_001354516.2 intron
NM_001354516.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.32
Genes affected
NDUFAF6 (HGNC:28625): (NADH:ubiquinone oxidoreductase complex assembly factor 6) This gene encodes a protein that localizes to mitochondria and contains a predicted phytoene synthase domain. The encoded protein plays an important role in the assembly of complex I (NADH-ubiquinone oxidoreductase) of the mitochondrial respiratory chain through regulation of subunit ND1 biogenesis. Mutations in this gene are associated with complex I enzymatic deficiency. [provided by RefSeq, Nov 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-1.0).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.698 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NDUFAF6 | NM_001354514.2 | c.-485-966G>A | intron_variant | ||||
NDUFAF6 | NM_001354515.2 | c.-268-966G>A | intron_variant | ||||
NDUFAF6 | NM_001354516.2 | c.-263-966G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NDUFAF6 | ENST00000396113.5 | c.-798-966G>A | intron_variant | 5 | |||||
NDUFAF6 | ENST00000519136.5 | c.-440-966G>A | intron_variant | 5 | |||||
NDUFAF6 | ENST00000523378.5 | c.-387-966G>A | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.496 AC: 75069AN: 151474Hom.: 18933 Cov.: 31
GnomAD3 genomes
?
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31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.496 AC: 75126AN: 151590Hom.: 18946 Cov.: 31 AF XY: 0.502 AC XY: 37155AN XY: 74072
GnomAD4 genome
?
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37155
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74072
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at