8-56073068-TC-T

Variant names:

• chr8-56073068-TC-T
• rs145164279
• NM_001023.4:c.*21delG

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BS1 BS2

The NM_001023.4(RPS20):​c.*21delG variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0124 in 1,587,442 control chromosomes in the GnomAD database, including 128 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.0090 (8 hom., cov: 32)
  • Exomes 𝑓: 0.013 (120 hom.)
• Consequence: RPS20 NM_001023.4 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.25

Genes affected

RPS20 (HGNC:10405): (ribosomal protein S20) 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 S10P family of ribosomal proteins. It is located in the cytoplasm. This gene is co-transcribed with the small nucleolar RNA gene U54, which is located in its second intron. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. Two transcript variants encoding different isoforms have been identified for this gene. [provided by RefSeq, Apr 2009]

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP6: Variant 8-56073068-TC-T is Benign according to our data. Variant chr8-56073068-TC-T is described in ClinVar as [Benign]. Clinvar id is 1802762.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population mid. GnomAdExome4 allele frequency = 0.0127 (18281/1435104) while in subpopulation MID AF = 0.0195 (80/4104). AF 95% confidence interval is 0.0161. There are 120 homozygotes in GnomAdExome4. There are 8913 alleles in the male GnomAdExome4 subpopulation. Median coverage is 30. This position FAILED quality control check.
• BS2: High AC in GnomAd4 at 1378 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RPS20	NM_001023.4	c.*21delG		3_prime_UTR_variant	Exon 4 of 4	ENST00000009589.8	NP_001014.1
RPS20	NM_001146227.3	c.333+48delG		intron_variant	Intron 4 of 5		NP_001139699.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RPS20	ENST00000009589	c.*21delG		3_prime_UTR_variant	Exon 4 of 4	1	NM_001023.4	ENSP00000009589.3

Frequencies

GnomAD3 genomes AF: 0.00907 AC: 1381 AN: 152220 Hom.: 8 Cov.: 32

Gnomad AFR AF: 0.00217

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.00759

Gnomad ASJ AF: 0.00577

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00684

Gnomad FIN AF: 0.0133

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0138

Gnomad OTH AF: 0.0115

GnomAD2 exomes AF: 0.0107 AC: 2478 AN: 231954 AF XY: 0.0108

Gnomad AFR exome AF: 0.00246

Gnomad AMR exome AF: 0.00899

Gnomad ASJ exome AF: 0.00427

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.0133

Gnomad NFE exome AF: 0.0145

Gnomad OTH exome AF: 0.0168

GnomAD4 exome AF: 0.0127 AC: 18281 AN: 1435104 Hom.: 120 Cov.: 30 AF XY: 0.0125 AC XY: 8913 AN XY: 713070

Gnomad4 AFR exome AF: 0.00227 AC: 75 AN: 33006

Gnomad4 AMR exome AF: 0.00886 AC: 381 AN: 43018

Gnomad4 ASJ exome AF: 0.00526 AC: 136 AN: 25832

Gnomad4 EAS exome AF: 0.0000253 AC: 1 AN: 39504

Gnomad4 SAS exome AF: 0.00856 AC: 732 AN: 85490

Gnomad4 FIN exome AF: 0.0141 AC: 551 AN: 39030

Gnomad4 NFE exome AF: 0.0141 AC: 15586 AN: 1105460

Gnomad4 Remaining exome AF: 0.0124 AC: 739 AN: 59660

GnomAD4 genome AF: 0.00905 AC: 1378 AN: 152338 Hom.: 8 Cov.: 32 AF XY: 0.00875 AC XY: 652 AN XY: 74492

Gnomad4 AFR AF: 0.00216 AC: 0.00216471 AN: 0.00216471

Gnomad4 AMR AF: 0.00758 AC: 0.0075817 AN: 0.0075817

Gnomad4 ASJ AF: 0.00577 AC: 0.00576701 AN: 0.00576701

Gnomad4 EAS AF: 0.00 AC: 0 AN: 0

Gnomad4 SAS AF: 0.00705 AC: 0.00705102 AN: 0.00705102

Gnomad4 FIN AF: 0.0133 AC: 0.0132668 AN: 0.0132668

Gnomad4 NFE AF: 0.0138 AC: 0.0137582 AN: 0.0137582

Gnomad4 OTH AF: 0.0114 AC: 0.0113529 AN: 0.0113529

Alfa AF: 0.00555 Hom.: 0

Bravo AF: 0.00870

Asia WGS AF: 0.00404 AC: 14 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Benign:1

Mar 04, 2025

Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
Mutation Taster		=85/15	polymorphism

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

LitVar

Other links and lift over

dbSNP: rs145164279; hg19: chr8-56985627;