8-95024960-T-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001354516.2(NDUFAF6):c.42-7035T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000732 in 1,284,168 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00040 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000029 ( 0 hom. )
Consequence
NDUFAF6
NM_001354516.2 intron
NM_001354516.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0180
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 Likely_benign. Variant got -4 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.58).
BP6
?
Variant 8-95024960-T-G is Benign according to our data. Variant chr8-95024960-T-G is described in ClinVar as [Likely_benign]. Clinvar id is 512921.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NDUFAF6 | NM_152416.4 | upstream_gene_variant | ENST00000396124.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NDUFAF6 | ENST00000396124.9 | upstream_gene_variant | 2 | NM_152416.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000401 AC: 61AN: 152148Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000617 AC: 1AN: 1620Hom.: 0 AF XY: 0.00112 AC XY: 1AN XY: 892
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GnomAD4 exome AF: 0.0000292 AC: 33AN: 1131902Hom.: 0 Cov.: 28 AF XY: 0.0000185 AC XY: 10AN XY: 540970
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GnomAD4 genome ? AF: 0.000401 AC: 61AN: 152266Hom.: 0 Cov.: 33 AF XY: 0.000336 AC XY: 25AN XY: 74458
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 08, 2017 | 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. - |
Computational scores
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Name
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Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at