16-57447523-A-G
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 2P and 15B. PM2BP4_ModerateBP6_Very_StrongBP7BS1
The NM_020312.4(COQ9):āc.18A>Gā(p.Val6=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000238 in 1,303,320 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Genomes: š 0.00011 ( 0 hom., cov: 34)
Exomes š: 0.000012 ( 0 hom. )
Consequence
COQ9
NM_020312.4 synonymous
NM_020312.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.150
Genes affected
COQ9 (HGNC:25302): (coenzyme Q9) This locus represents a mitochondrial ubiquinone biosynthesis gene. The encoded protein is likely necessary for biosynthesis of coenzyme Q10, as mutations at this locus have been associated with autosomal-recessive neonatal-onset primary coenzyme Q10 deficiency.[provided by RefSeq, Sep 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.42).
BP6
Variant 16-57447523-A-G is Benign according to our data. Variant chr16-57447523-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 509392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=0.15 with no splicing effect.
BS1
Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.000112 (17/151906) while in subpopulation AMR AF= 0.000916 (14/15286). AF 95% confidence interval is 0.000553. There are 0 homozygotes in gnomad4. There are 8 alleles in male gnomad4 subpopulation. Median coverage is 34. This position pass quality control queck.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COQ9 | NM_020312.4 | c.18A>G | p.Val6= | synonymous_variant | 1/9 | ENST00000262507.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COQ9 | ENST00000262507.11 | c.18A>G | p.Val6= | synonymous_variant | 1/9 | 1 | NM_020312.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000112 AC: 17AN: 151782Hom.: 0 Cov.: 34
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GnomAD3 exomes AF: 0.0000210 AC: 1AN: 47638Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 27424
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GnomAD4 exome AF: 0.0000122 AC: 14AN: 1151414Hom.: 0 Cov.: 32 AF XY: 0.00000720 AC XY: 4AN XY: 555934
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GnomAD4 genome AF: 0.000112 AC: 17AN: 151906Hom.: 0 Cov.: 34 AF XY: 0.000108 AC XY: 8AN XY: 74268
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 14, 2017 | 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. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 04, 2023 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at