chr1-46673908-C-G
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The 1-46673908-C-G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.797 in 158,430 control chromosomes in the GnomAD database, including 50,525 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 0.80 ( 48606 hom., cov: 33)
Exomes 𝑓: 0.79 ( 1919 hom. )
Consequence
ATPAF1
ENST00000525633.1 upstream_gene
ENST00000525633.1 upstream_gene
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.22
Genes affected
ATPAF1 (HGNC:18803): (ATP synthase mitochondrial F1 complex assembly factor 1) This gene encodes an assembly factor for the F(1) component of the mitochondrial ATP synthase. This protein binds specifically to the F1 beta subunit and is thought to prevent this subunit from forming nonproductive homooligomers during enzyme assembly. Alternatively spliced transcript variants have been identified. [provided by RefSeq, Aug 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=-0.88).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.891 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
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Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATPAF1 | ENST00000525633.1 | upstream_gene_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.798 AC: 121367AN: 152162Hom.: 48533 Cov.: 33
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GnomAD4 exome AF: 0.786 AC: 4834AN: 6150Hom.: 1919 Cov.: 0 AF XY: 0.785 AC XY: 2438AN XY: 3104
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GnomAD4 genome AF: 0.798 AC: 121497AN: 152280Hom.: 48606 Cov.: 33 AF XY: 0.801 AC XY: 59618AN XY: 74464
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at