chr8-95024928-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001354516.2(NDUFAF6):c.42-7067A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 1,185,828 control chromosomes in the GnomAD database, including 11,935 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.15 ( 1642 hom., cov: 33)
Exomes 𝑓: 0.14 ( 10293 hom. )
Consequence
NDUFAF6
NM_001354516.2 intron
NM_001354516.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.671
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP6
?
Variant 8-95024928-A-G is Benign according to our data. Variant chr8-95024928-A-G is described in ClinVar as [Benign]. Clinvar id is 1292143.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NDUFAF6 | NM_001354514.2 | c.-83-7067A>G | intron_variant | ||||
NDUFAF6 | NM_001354515.2 | c.-83-7067A>G | intron_variant | ||||
NDUFAF6 | NM_001354516.2 | c.42-7067A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NDUFAF6 | ENST00000396111.6 | c.-83-7067A>G | intron_variant | 5 | |||||
NDUFAF6 | ENST00000396113.5 | c.-84+1609A>G | intron_variant | 5 | |||||
NDUFAF6 | ENST00000519136.5 | c.-255-7067A>G | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.146 AC: 22214AN: 152036Hom.: 1641 Cov.: 33
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GnomAD4 exome AF: 0.139 AC: 143829AN: 1033674Hom.: 10293 AF XY: 0.139 AC XY: 68504AN XY: 494170
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GnomAD4 genome ? AF: 0.146 AC: 22228AN: 152154Hom.: 1642 Cov.: 33 AF XY: 0.148 AC XY: 10996AN XY: 74396
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 26, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at