4-83284851-T-G
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_015697.9(COQ2):c.64A>C(p.Arg22Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000534 in 1,547,008 control chromosomes in the GnomAD database, including 12 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_015697.9 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COQ2 | ENST00000311469.9 | c.64A>C | p.Arg22Arg | synonymous_variant | Exon 1 of 7 | 1 | ENSP00000310873.4 | |||
COQ2 | ENST00000647002.2 | c.-87A>C | upstream_gene_variant | NM_001358921.2 | ENSP00000495761.2 | |||||
COQ2 | ENST00000311461.7 | c.-87A>C | upstream_gene_variant | 5 | ENSP00000311835.7 | |||||
COQ2 | ENST00000503391.5 | n.-87A>C | upstream_gene_variant | 2 | ENSP00000426242.1 |
Frequencies
GnomAD3 genomes AF: 0.000512 AC: 78AN: 152198Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00395 AC: 609AN: 154366Hom.: 9 AF XY: 0.00279 AC XY: 235AN XY: 84120
GnomAD4 exome AF: 0.000536 AC: 748AN: 1394696Hom.: 11 Cov.: 33 AF XY: 0.000431 AC XY: 297AN XY: 689648
GnomAD4 genome AF: 0.000512 AC: 78AN: 152312Hom.: 1 Cov.: 32 AF XY: 0.000456 AC XY: 34AN XY: 74486
ClinVar
Submissions by phenotype
not specified Benign:2
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. -
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not provided Benign:2
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at