chr14-103563036-T-TC
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PVS1_StrongPM2PP5_Moderate
The NM_001370595.2(COA8):c.41dup(p.Leu15SerfsTer40) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000388 in 1,544,574 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. L12L) has been classified as Likely benign.
Frequency
Consequence
NM_001370595.2 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COA8 | NM_001370595.2 | c.41dup | p.Leu15SerfsTer40 | frameshift_variant | 1/5 | ENST00000409074.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COA8 | ENST00000409074.8 | c.41dup | p.Leu15SerfsTer40 | frameshift_variant | 1/5 | 1 | NM_001370595.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 152050Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.00000692 AC: 1AN: 144414Hom.: 0 AF XY: 0.0000126 AC XY: 1AN XY: 79136
GnomAD4 exome AF: 0.00000359 AC: 5AN: 1392524Hom.: 0 Cov.: 32 AF XY: 0.00000726 AC XY: 5AN XY: 688328
GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 152050Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 74280
ClinVar
Submissions by phenotype
Mitochondrial complex IV deficiency, nuclear type 1 Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Genomic Research Center, Shahid Beheshti University of Medical Sciences | Apr 27, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at