14-70329183-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_016468.7(COX16):c.195G>A(p.Ser65Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000661 in 1,588,980 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 (★).
Frequency
Consequence
NM_016468.7 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COX16 | ENST00000389912.7 | c.195G>A | p.Ser65Ser | synonymous_variant | Exon 3 of 4 | 1 | NM_016468.7 | ENSP00000374562.5 | ||
SYNJ2BP-COX16 | ENST00000621525.4 | c.423G>A | p.Ser141Ser | synonymous_variant | Exon 5 of 6 | 2 | ENSP00000482133.1 |
Frequencies
GnomAD3 genomes AF: 0.000324 AC: 49AN: 151046Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000974 AC: 24AN: 246380Hom.: 0 AF XY: 0.0000375 AC XY: 5AN XY: 133424
GnomAD4 exome AF: 0.0000389 AC: 56AN: 1437934Hom.: 0 Cov.: 30 AF XY: 0.0000266 AC XY: 19AN XY: 715058
GnomAD4 genome AF: 0.000324 AC: 49AN: 151046Hom.: 0 Cov.: 31 AF XY: 0.000516 AC XY: 38AN XY: 73714
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at