chr17-47828531-G-A
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Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_145255.4(MRPL10):c.192C>T(p.Cys64=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000183 in 1,461,174 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0010 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000086 ( 1 hom. )
Consequence
MRPL10
NM_145255.4 synonymous
NM_145255.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.16
Genes affected
MRPL10 (HGNC:14055): (mitochondrial ribosomal protein L10) 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 39S subunit protein. Sequence analysis identified three transcript variants that encode two different isoforms. A pseudogene corresponding to this gene is found on chromosome 5q. [provided by RefSeq, Nov 2010]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.44).
BP6
Variant 17-47828531-G-A is Benign according to our data. Variant chr17-47828531-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3039902.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=1.16 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MRPL10 | NM_145255.4 | c.192C>T | p.Cys64= | synonymous_variant | 2/5 | ENST00000351111.7 | |
MRPL10 | NM_148887.3 | c.222C>T | p.Cys74= | synonymous_variant | 3/6 | ||
MRPL10 | XM_024450575.2 | c.222C>T | p.Cys74= | synonymous_variant | 3/6 | ||
MRPL10 | NR_037575.2 | n.371C>T | non_coding_transcript_exon_variant | 2/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MRPL10 | ENST00000351111.7 | c.192C>T | p.Cys64= | synonymous_variant | 2/5 | 1 | NM_145255.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00102 AC: 156AN: 152206Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000336 AC: 51AN: 151620Hom.: 0 AF XY: 0.000264 AC XY: 22AN XY: 83382
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GnomAD4 exome AF: 0.0000856 AC: 112AN: 1308850Hom.: 1 Cov.: 32 AF XY: 0.0000593 AC XY: 38AN XY: 640638
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GnomAD4 genome AF: 0.00102 AC: 156AN: 152324Hom.: 0 Cov.: 32 AF XY: 0.000967 AC XY: 72AN XY: 74486
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
MRPL10-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 28, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at