17-57840938-G-A
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BA1
The NM_016070.4(MRPS23):c.408C>T(p.Gly136=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00286 in 1,613,974 control chromosomes in the GnomAD database, including 106 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.015 ( 47 hom., cov: 33)
Exomes 𝑓: 0.0016 ( 59 hom. )
Consequence
MRPS23
NM_016070.4 synonymous
NM_016070.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.852
Genes affected
MRPS23 (HGNC:14509): (mitochondrial ribosomal protein S23) 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. A pseudogene corresponding to this gene is found on chromosome 7p. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.34).
BP6
?
Variant 17-57840938-G-A is Benign according to our data. Variant chr17-57840938-G-A is described in ClinVar as [Benign]. Clinvar id is 1529603.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.852 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0517 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MRPS23 | NM_016070.4 | c.408C>T | p.Gly136= | synonymous_variant | 4/5 | ENST00000313608.13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MRPS23 | ENST00000313608.13 | c.408C>T | p.Gly136= | synonymous_variant | 4/5 | 1 | NM_016070.4 | P1 | |
MRPS23 | ENST00000578444.1 | c.408C>T | p.Gly136= | synonymous_variant | 4/4 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0152 AC: 2312AN: 152064Hom.: 47 Cov.: 33
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GnomAD3 exomes AF: 0.00391 AC: 983AN: 251328Hom.: 21 AF XY: 0.00293 AC XY: 398AN XY: 135836
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GnomAD4 exome AF: 0.00157 AC: 2302AN: 1461792Hom.: 59 Cov.: 31 AF XY: 0.00136 AC XY: 986AN XY: 727188
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GnomAD4 genome ? AF: 0.0152 AC: 2316AN: 152182Hom.: 47 Cov.: 33 AF XY: 0.0145 AC XY: 1082AN XY: 74400
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 04, 2024 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
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Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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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