GeneBe

rs226202

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001025.5(RPS23):​c.*259G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

RPS23
NM_001025.5 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.61

Publications

31 publications found
Variant links:
Genes affected
RPS23 (HGNC:10410): (ribosomal protein S23) 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 S12P family of ribosomal proteins. It is located in the cytoplasm. The protein shares significant amino acid similarity with S. cerevisiae ribosomal protein S28. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. [provided by RefSeq, Jul 2008]
ATG10 (HGNC:20315): (autophagy related 10) Autophagy is a process for the bulk degradation of cytosolic compartments by lysosomes. ATG10 is an E2-like enzyme involved in 2 ubiquitin-like modifications essential for autophagosome formation: ATG12 (MIM 609608)-ATG5 (MIM 604261) conjugation and modification of a soluble form of MAP-LC3 (MAP1LC3A; MIM 601242), a homolog of yeast Apg8, to a membrane-bound form (Nemoto et al., 2003 [PubMed 12890687]).[supplied by OMIM, Mar 2008]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001025.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
RPS23
NM_001025.5
MANE Select
c.*259G>T
3_prime_UTR
Exon 4 of 4NP_001016.1

Ensembl Transcripts

Selected
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
RPS23
ENST00000296674.13
TSL:1 MANE Select
c.*259G>T
3_prime_UTR
Exon 4 of 4ENSP00000296674.8
RPS23
ENST00000651545.1
c.*259G>T
3_prime_UTR
Exon 4 of 5ENSP00000498621.1
RPS23
ENST00000510019.5
TSL:4
c.*259G>T
3_prime_UTR
Exon 4 of 4ENSP00000425833.1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
284940
Hom.:
0
Cov.:
2
AF XY:
0.00
AC XY:
0
AN XY:
147434
African (AFR)
AF:
0.00
AC:
0
AN:
8390
American (AMR)
AF:
0.00
AC:
0
AN:
9946
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
9588
East Asian (EAS)
AF:
0.00
AC:
0
AN:
20926
South Asian (SAS)
AF:
0.00
AC:
0
AN:
17130
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
21724
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
1346
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
178262
Other (OTH)
AF:
0.00
AC:
0
AN:
17628
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.13
DANN
Benign
0.39
PhyloP100
-3.6

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs226202; hg19: chr5-81571669; API