8-144792101-T-C

Variant names:

• chr8-144792101-T-C
• rs1234028238
• NM_001317782.2:c.29A>G

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_001317782.2(RPL8):​c.29A>G​(p.Lys10Arg) variant causes a missense change. The variant allele was found at a frequency of 0.000000696 in 1,437,632 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 7.0e-7 (0 hom.)
• Consequence: RPL8 NM_001317782.2 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 4.86

Genes affected

RPL8 (HGNC:10368): (ribosomal protein L8) 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 60S subunit. The protein belongs to the L2P family of ribosomal proteins. It is located in the cytoplasm. In rat, the protein associates with the 5.8S rRNA, very likely participates in the binding of aminoacyl-tRNA, and is a constituent of the elongation factor 2-binding site at the ribosomal subunit interface. Alternatively spliced transcript variants encoding the same protein exist. 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]

MIR6850 (HGNC:50093): (microRNA 6850) microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RPL8	NM_001317782.2	c.29A>G	p.Lys10Arg	missense_variant	Exon 1 of 5	ENST00000528957.6	NP_001304711.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RPL8	ENST00000528957.6	c.29A>G	p.Lys10Arg	missense_variant	Exon 1 of 5	1	NM_001317782.2	ENSP00000433464.2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD2 exomes AF: 0.00000459 AC: 1 AN: 217838 AF XY: 0.00000828

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000101

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 6.96e-7 AC: 1 AN: 1437632 Hom.: 0 Cov.: 32 AF XY: 0.00000140 AC XY: 1 AN XY: 714468

Gnomad4 AFR exome AF: 0.00 AC: 0 AN: 32728

Gnomad4 AMR exome AF: 0.00 AC: 0 AN: 41550

Gnomad4 ASJ exome AF: 0.00 AC: 0 AN: 25202

Gnomad4 EAS exome AF: 0.00 AC: 0 AN: 39394

Gnomad4 SAS exome AF: 0.00 AC: 0 AN: 84632

Gnomad4 FIN exome AF: 0.00 AC: 0 AN: 45684

Gnomad4 NFE exome AF: 0.00 AC: 0 AN: 1103376

Gnomad4 Remaining exome AF: 0.0000168 AC: 1 AN: 59380

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000756

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Oct 13, 2023

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.29A>G (p.K10R) alteration is located in exon 2 (coding exon 1) of the RPL8 gene. This alteration results from a A to G substitution at nucleotide position 29, causing the lysine (K) at amino acid position 10 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.19
BayesDel_addAF	Benign	-0.11	T
BayesDel_noAF	Benign	-0.39
CADD	Pathogenic	26
DANN	Uncertain	0.99
DEOGEN2	Benign	0.077	T;T;T;T;.;T
Eigen	Benign	0.089
Eigen_PC	Uncertain	0.22
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Pathogenic	0.98	.;D;.;D;D;D
M_CAP	Benign	0.0058	T
MetaRNN	Uncertain	0.43	T;T;T;T;T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Uncertain	2.8	M;.;M;M;.;.
PrimateAI	Pathogenic	0.91	D
PROVEAN	Uncertain	-2.6	D;N;D;N;N;N
REVEL	Benign	0.15
Sift	Uncertain	0.029	D;D;D;D;D;D
Sift4G	Benign	0.89	T;T;T;T;.;T
Polyphen		0.45	P;.;P;P;.;.
Vest4		0.60
MutPred		0.29		Loss of ubiquitination at K10 (P = 0.0381);Loss of ubiquitination at K10 (P = 0.0381);Loss of ubiquitination at K10 (P = 0.0381);Loss of ubiquitination at K10 (P = 0.0381);Loss of ubiquitination at K10 (P = 0.0381);Loss of ubiquitination at K10 (P = 0.0381);
MVP		0.68
MPC		0.79
ClinPred		0.89	D
GERP RS		5.0
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.56
gMVP		0.69
Mutation Taster		=50/50

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs1234028238; hg19: chr8-146017486;