NM_001025.5:c.*82C>T

Variant names:

• chr5-82276027-G-A
• rs226201
• NM_001025.5:c.*82C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001025.5(RPS23):​c.*82C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.566 in 1,319,230 control chromosomes in the GnomAD database, including 221,972 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 0.47 (20487 hom., cov: 31)
  • Exomes 𝑓: 0.58 (201485 hom.)
• Consequence: RPS23 NM_001025.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.107
• Publications: 24 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.886 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RPS23	NM_001025.5	c.*82C>T		3_prime_UTR_variant	Exon 4 of 4	ENST00000296674.13	NP_001016.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RPS23	ENST00000296674.13	c.*82C>T		3_prime_UTR_variant	Exon 4 of 4	1	NM_001025.5	ENSP00000296674.8

Frequencies

GnomAD3 genomes AF: 0.474 AC: 72043 AN: 151846 Hom.: 20464 Cov.: 31

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.327

Gnomad AMR AF: 0.639

Gnomad ASJ AF: 0.468

Gnomad EAS AF: 0.907

Gnomad SAS AF: 0.665

Gnomad FIN AF: 0.586

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.495

GnomAD4 exome AF: 0.578 AC: 675202 AN: 1167266 Hom.: 201485 Cov.: 15 AF XY: 0.582 AC XY: 339824 AN XY: 584234

African (AFR) AF: 0.141 AC: 3679 AN: 26048

American (AMR) AF: 0.729 AC: 21803 AN: 29916

Ashkenazi Jewish (ASJ) AF: 0.472 AC: 9346 AN: 19804

East Asian (EAS) AF: 0.936 AC: 35676 AN: 38106

South Asian (SAS) AF: 0.651 AC: 43567 AN: 66936

European-Finnish (FIN) AF: 0.583 AC: 29226 AN: 50126

Middle Eastern (MID) AF: 0.525 AC: 1747 AN: 3326

European-Non Finnish (NFE) AF: 0.569 AC: 502512 AN: 883274

Other (OTH) AF: 0.556 AC: 27646 AN: 49730

GnomAD4 genome AF: 0.474 AC: 72077 AN: 151964 Hom.: 20487 Cov.: 31 AF XY: 0.483 AC XY: 35902 AN XY: 74274

African (AFR) AF: 0.158 AC: 6548 AN: 41460

American (AMR) AF: 0.640 AC: 9766 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.468 AC: 1623 AN: 3470

East Asian (EAS) AF: 0.908 AC: 4692 AN: 5170

South Asian (SAS) AF: 0.666 AC: 3202 AN: 4810

European-Finnish (FIN) AF: 0.586 AC: 6176 AN: 10534

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.568 AC: 38579 AN: 67946

Other (OTH) AF: 0.499 AC: 1052 AN: 2108

Alfa AF: 0.549 Hom.: 12506

Bravo AF: 0.465

Asia WGS AF: 0.750 AC: 2607 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.2
DANN	Benign	0.65
PhyloP100		0.11
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.2
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs226201; hg19: chr5-81571846;