10-73250938-GTC-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_016065.4(MRPS16):c.326_327delGA(p.Arg109ThrfsTer8) variant causes a frameshift change. The variant allele was found at a frequency of 0.0000229 in 1,614,052 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_016065.4 frameshift
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MRPS16 | NM_016065.4 | c.326_327delGA | p.Arg109ThrfsTer8 | frameshift_variant | Exon 3 of 3 | ENST00000372945.8 | NP_057149.1 | |
MRPS16 | XM_047425263.1 | c.320_321delGA | p.Arg107ThrfsTer8 | frameshift_variant | Exon 3 of 3 | XP_047281219.1 | ||
MRPS16 | NM_001410935.1 | c.274+823_274+824delGA | intron_variant | Intron 2 of 2 | NP_001397864.1 | |||
DNAJC9-AS1 | NR_038373.1 | n.175+2493_175+2494delTC | intron_variant | Intron 2 of 3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152176Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000994 AC: 25AN: 251488Hom.: 0 AF XY: 0.0000736 AC XY: 10AN XY: 135918
GnomAD4 exome AF: 0.0000233 AC: 34AN: 1461876Hom.: 0 AF XY: 0.0000193 AC XY: 14AN XY: 727238
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152176Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74348
ClinVar
Submissions by phenotype
not provided Uncertain:1
This sequence change creates a premature translational stop signal (p.Arg109Thrfs*8) in the MRPS16 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 29 amino acid(s) of the MRPS16 protein. This variant is present in population databases (rs762604257, gnomAD 0.07%), and has an allele count higher than expected for a pathogenic variant. This variant has not been reported in the literature in individuals affected with MRPS16-related conditions. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at