rs763983826
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_016065.4(MRPS16):c.290dupT(p.Leu99SerfsTer10) variant causes a frameshift change. The variant allele was found at a frequency of 0.0000062 in 1,614,006 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
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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.290dupT | p.Leu99SerfsTer10 | frameshift_variant | Exon 3 of 3 | ENST00000372945.8 | NP_057149.1 | |
MRPS16 | XM_047425263.1 | c.284dupT | p.Leu97SerfsTer10 | frameshift_variant | Exon 3 of 3 | XP_047281219.1 | ||
MRPS16 | NM_001410935.1 | c.274+787dupT | intron_variant | Intron 2 of 2 | NP_001397864.1 | |||
DNAJC9-AS1 | NR_038373.1 | n.175+2530dupA | intron_variant | Intron 2 of 3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152140Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251444Hom.: 0 AF XY: 0.0000441 AC XY: 6AN XY: 135904
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461866Hom.: 0 Cov.: 31 AF XY: 0.00000825 AC XY: 6AN XY: 727232
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152140Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74326
ClinVar
Submissions by phenotype
not provided Uncertain:1
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. This sequence change creates a premature translational stop signal (p.Leu99Serfs*10) in the MRPS16 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 39 amino acid(s) of the MRPS16 protein. This variant is present in population databases (rs763983826, gnomAD 0.03%). This variant has not been reported in the literature in individuals affected with MRPS16-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at