chr12-4654234-G-C
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_005002.5(NDUFA9):c.50-58G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.262 in 1,493,716 control chromosomes in the GnomAD database, including 52,778 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). There are indicators that this mutation may affect the branch point..
Frequency
Genomes: 𝑓 0.26 ( 5486 hom., cov: 33)
Exomes 𝑓: 0.26 ( 47292 hom. )
Consequence
NDUFA9
NM_005002.5 intron
NM_005002.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.120
Genes affected
NDUFA9 (HGNC:7693): (NADH:ubiquinone oxidoreductase subunit A9) The encoded protein is a subunit of the hydrophobic protein fraction of the NADH:ubiquinone oxidoreductase (complex I), the first enzyme complex in the electron transport chain located in the inner mitochondrial membrane. A pseudogene has been identified on chromosome 12. [provided by RefSeq, May 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
This place is a probable branch point but likely benign (scored 1 / 10). Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BP6
Variant 12-4654234-G-C is Benign according to our data. Variant chr12-4654234-G-C is described in ClinVar as [Benign]. Clinvar id is 1290676.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.279 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NDUFA9 | NM_005002.5 | c.50-58G>C | intron_variant | ENST00000266544.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NDUFA9 | ENST00000266544.10 | c.50-58G>C | intron_variant | 1 | NM_005002.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.265 AC: 40268AN: 151982Hom.: 5489 Cov.: 33
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GnomAD4 exome AF: 0.262 AC: 351156AN: 1341616Hom.: 47292 AF XY: 0.261 AC XY: 172791AN XY: 663026
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GnomAD4 genome AF: 0.265 AC: 40291AN: 152100Hom.: 5486 Cov.: 33 AF XY: 0.258 AC XY: 19167AN XY: 74354
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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 23, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
BranchPoint Hunter
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at