rs12247015
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The 10-58385319-A-G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.421 in 605,450 control chromosomes in the GnomAD database, including 59,162 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.49 ( 20812 hom., cov: 33)
Exomes 𝑓: 0.40 ( 38350 hom. )
Consequence
TFAM
ENST00000373899.3 upstream_gene
ENST00000373899.3 upstream_gene
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.03
Genes affected
TFAM (HGNC:11741): (transcription factor A, mitochondrial) This gene encodes a key mitochondrial transcription factor containing two high mobility group motifs. The encoded protein also functions in mitochondrial DNA replication and repair. Sequence polymorphisms in this gene are associated with Alzheimer's and Parkinson's diseases. There are pseudogenes for this gene on chromosomes 6, 7, and 11. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2012]
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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=-0.85).
BP6
?
Variant 10-58385319-A-G is Benign according to our data. Variant chr10-58385319-A-G is described in ClinVar as [Benign]. Clinvar id is 684177.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.747 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TFAM | ENST00000373899.3 | upstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.493 AC: 75019AN: 152022Hom.: 20792 Cov.: 33
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GnomAD4 exome AF: 0.397 AC: 179797AN: 453310Hom.: 38350 Cov.: 2 AF XY: 0.393 AC XY: 94647AN XY: 240946
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GnomAD4 genome ? AF: 0.494 AC: 75083AN: 152140Hom.: 20812 Cov.: 33 AF XY: 0.482 AC XY: 35840AN XY: 74364
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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 14, 2018 | 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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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