chr10-73249995-CAGG-C
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_016065.4(MRPS16):c.*854_*856del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000199 in 150,812 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000020 ( 0 hom., cov: 32)
Consequence
MRPS16
NM_016065.4 3_prime_UTR
NM_016065.4 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.644
Genes affected
MRPS16 (HGNC:14048): (mitochondrial ribosomal protein S16) Mammalian mitochondrial ribosomal proteins are encoded by nuclear genes and help in protein synthesis within the mitochondrion. Mitochondrial ribosomes (mitoribosomes) consist of a small 28S subunit and a large 39S subunit. They have an estimated 75% protein to rRNA composition compared to prokaryotic ribosomes, where this ratio is reversed. Another difference between mammalian mitoribosomes and prokaryotic ribosomes is that the latter contain a 5S rRNA. Among different species, the proteins comprising the mitoribosome differ greatly in sequence, and sometimes in biochemical properties, which prevents easy recognition by sequence homology. This gene encodes a 28S subunit protein that belongs to the ribosomal protein S16P family. The encoded protein is one of the most highly conserved ribosomal proteins between mammalian and yeast mitochondria. Three pseudogenes (located at 8q21.3, 20q13.32, 22q12-q13.1) for this gene have been described. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MRPS16 | NM_016065.4 | c.*854_*856del | 3_prime_UTR_variant | 3/3 | ENST00000372945.8 | ||
DNAJC9-AS1 | NR_038373.1 | n.175+1548_175+1550del | intron_variant, non_coding_transcript_variant | ||||
MRPS16 | XM_047425263.1 | c.*854_*856del | 3_prime_UTR_variant | 3/3 | |||
MRPS16 | NM_001410935.1 | c.275-680_275-678del | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MRPS16 | ENST00000372945.8 | c.*854_*856del | 3_prime_UTR_variant | 3/3 | 1 | NM_016065.4 | P1 | ||
DNAJC9-AS1 | ENST00000440197.2 | n.182+1548_182+1550del | intron_variant, non_coding_transcript_variant | 1 | |||||
MRPS16 | ENST00000372940.3 | c.275-680_275-678del | intron_variant | 2 | |||||
MRPS16 | ENST00000479005.1 | n.1425_1427del | non_coding_transcript_exon_variant | 3/3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000199 AC: 3AN: 150812Hom.: 0 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.0000199 AC: 3AN: 150812Hom.: 0 Cov.: 32 AF XY: 0.0000271 AC XY: 2AN XY: 73746
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Combined oxidative phosphorylation deficiency Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at