chr6-34424787-G-A
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Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_001014.5(RPS10):c.204C>T(p.Tyr68Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000223 in 1,614,146 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 Likely benign (★★).
Frequency
Genomes: 𝑓 0.000046 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000020 ( 0 hom. )
Consequence
RPS10
NM_001014.5 synonymous
NM_001014.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.07
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]
RPS10-NUDT3 (HGNC:49181): (RPS10-NUDT3 readthrough) This locus represents naturally occurring read-through transcription between the neighboring RPS10 (ribosomal protein S10) and NUDT3 (nudix (nucleoside diphosphate linked moiety X)-type motif 3) genes on chromosome 6. The read-through transcript produces a fusion protein that shares sequence identity with each individual gene product. [provided by RefSeq, Feb 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -17 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.59).
BP6
Variant 6-34424787-G-A is Benign according to our data. Variant chr6-34424787-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 463370.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=2.07 with no splicing effect.
BS2
High AC in GnomAd4 at 7 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RPS10 | NM_001014.5 | c.204C>T | p.Tyr68Tyr | synonymous_variant | 3/6 | ENST00000648437.1 | NP_001005.1 | |
RPS10-NUDT3 | NM_001202470.3 | c.204C>T | p.Tyr68Tyr | synonymous_variant | 3/9 | NP_001189399.1 | ||
RPS10 | NM_001203245.3 | c.204C>T | p.Tyr68Tyr | synonymous_variant | 3/6 | NP_001190174.1 | ||
RPS10 | NM_001204091.2 | c.204C>T | p.Tyr68Tyr | synonymous_variant | 3/6 | NP_001191020.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RPS10 | ENST00000648437.1 | c.204C>T | p.Tyr68Tyr | synonymous_variant | 3/6 | NM_001014.5 | ENSP00000497917.1 | |||
RPS10-NUDT3 | ENST00000639725.1 | c.204C>T | p.Tyr68Tyr | synonymous_variant | 3/9 | 5 | ENSP00000492441.1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152222Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000240 AC: 6AN: 250428Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135644
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GnomAD4 exome AF: 0.0000198 AC: 29AN: 1461806Hom.: 0 Cov.: 31 AF XY: 0.0000165 AC XY: 12AN XY: 727208
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GnomAD4 genome AF: 0.0000459 AC: 7AN: 152340Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74498
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Nov 07, 2018 | - - |
Diamond-Blackfan anemia 9 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Feb 24, 2022 | - - |
RPS10-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 15, 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). - |
Diamond-Blackfan anemia Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 01, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
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DANN
Benign
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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