rs3209
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_145255.4(MRPL10):c.*448A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.282 in 211,732 control chromosomes in the GnomAD database, including 10,184 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.27 ( 6956 hom., cov: 33)
Exomes 𝑓: 0.31 ( 3228 hom. )
Consequence
MRPL10
NM_145255.4 3_prime_UTR
NM_145255.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.32
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 Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.376 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MRPL10 | NM_145255.4 | c.*448A>G | 3_prime_UTR_variant | 5/5 | ENST00000351111.7 | ||
MRPL10 | NM_148887.3 | c.*448A>G | 3_prime_UTR_variant | 6/6 | |||
MRPL10 | XM_024450575.2 | c.*448A>G | 3_prime_UTR_variant | 6/6 | |||
MRPL10 | NR_037575.2 | n.1413A>G | non_coding_transcript_exon_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MRPL10 | ENST00000351111.7 | c.*448A>G | 3_prime_UTR_variant | 5/5 | 1 | NM_145255.4 | P1 | ||
MRPL10 | ENST00000290208.11 | c.*448A>G | 3_prime_UTR_variant | 5/5 | 2 | ||||
MRPL10 | ENST00000414011.1 | c.*448A>G | 3_prime_UTR_variant | 6/6 | 3 | ||||
MRPL10 | ENST00000421763.5 | c.*1236A>G | 3_prime_UTR_variant, NMD_transcript_variant | 5/5 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.272 AC: 41295AN: 152084Hom.: 6954 Cov.: 33
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GnomAD4 exome AF: 0.309 AC: 18380AN: 59530Hom.: 3228 Cov.: 0 AF XY: 0.294 AC XY: 9404AN XY: 31974
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GnomAD4 genome ? AF: 0.271 AC: 41314AN: 152202Hom.: 6956 Cov.: 33 AF XY: 0.270 AC XY: 20058AN XY: 74404
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at