rs781484971
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6BP7BS2
The NM_001014.5(RPS10):c.261G>A(p.Pro87=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000576 in 1,614,128 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.000079 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000055 ( 0 hom. )
Consequence
RPS10
NM_001014.5 synonymous
NM_001014.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.17
Genes affected
RPS10 (HGNC:10383): (ribosomal protein S10) Ribosomes, the organelles that catalyze protein synthesis, consist of a small 40S subunit and a large 60S subunit. Together these subunits are composed of 4 RNA species and approximately 80 structurally distinct proteins. This gene encodes a ribosomal protein that is a component of the 40S subunit. The protein belongs to the S10E family of ribosomal proteins. It is located in the cytoplasm. Variable expression of this gene in colorectal cancers compared to adjacent normal tissues has been observed, although no correlation between the level of expression and the severity of the disease has been found. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. Alternate splicing results in multiple transcript variants that encode the same protein. Naturally occurring read-through transcription occurs between this locus and the neighboring locus NUDT3 (nudix (nucleoside diphosphate linked moiety X)-type motif 3).[provided by RefSeq, Feb 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.62).
BP6
?
Variant 6-34424730-C-T is Benign according to our data. Variant chr6-34424730-C-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 463371.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=2, Uncertain_significance=2}.
BP7
?
Synonymous conserved (PhyloP=-2.17 with no splicing effect.
BS2
?
High AC in GnomAd4 at 12 AD gene.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
|---|---|---|---|---|---|---|---|
| RPS10 | NM_001014.5 | c.261G>A | p.Pro87= | synonymous_variant | 3/6 | ENST00000648437.1 | |
| RPS10-NUDT3 | NM_001202470.3 | c.261G>A | p.Pro87= | synonymous_variant | 3/9 | ||
| RPS10 | NM_001203245.3 | c.261G>A | p.Pro87= | synonymous_variant | 3/6 | ||
| RPS10 | NM_001204091.2 | c.261G>A | p.Pro87= | synonymous_variant | 3/6 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| RPS10 | ENST00000648437.1 | c.261G>A | p.Pro87= | synonymous_variant | 3/6 | NM_001014.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000788 AC: 12AN: 152206Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000799 AC: 20AN: 250264Hom.: 0 AF XY: 0.0000811 AC XY: 11AN XY: 135618
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GnomAD4 exome AF: 0.0000554 AC: 81AN: 1461804Hom.: 0 Cov.: 31 AF XY: 0.0000578 AC XY: 42AN XY: 727206
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GnomAD4 genome ? AF: 0.0000788 AC: 12AN: 152324Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74482
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:2Benign:2
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
Diamond-Blackfan anemia Benign:2
| Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 20, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
| Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
not specified Uncertain:1
| Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | May 13, 2019 | - - |
Diamond-Blackfan anemia 9 Uncertain:1
| Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Jan 04, 2022 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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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