rs12222188
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_012239.6(SIRT3):c.969+15C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0464 in 1,602,992 control chromosomes in the GnomAD database, including 2,692 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 0.048 ( 338 hom., cov: 31)
Exomes 𝑓: 0.046 ( 2354 hom. )
Consequence
SIRT3
NM_012239.6 intron
NM_012239.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.503
Genes affected
SIRT3 (HGNC:14931): (sirtuin 3) SIRT3 encodes a member of the sirtuin family of class III histone deacetylases, homologs to the yeast Sir2 protein. The encoded protein is found exclusively in mitochondria, where it can eliminate reactive oxygen species, inhibit apoptosis, and prevent the formation of cancer cells. SIRT3 has far-reaching effects on nuclear gene expression, cancer, cardiovascular disease, neuroprotection, aging, and metabolic control. [provided by RefSeq, May 2019]
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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=-0.83).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.132 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0477 AC: 7163AN: 150284Hom.: 338 Cov.: 31
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GnomAD3 exomes AF: 0.0564 AC: 14133AN: 250800Hom.: 595 AF XY: 0.0575 AC XY: 7796AN XY: 135624
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GnomAD4 exome AF: 0.0462 AC: 67174AN: 1452590Hom.: 2354 Cov.: 33 AF XY: 0.0472 AC XY: 34047AN XY: 721970
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GnomAD4 genome AF: 0.0477 AC: 7172AN: 150402Hom.: 338 Cov.: 31 AF XY: 0.0479 AC XY: 3522AN XY: 73490
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at