11-810882-G-T

Variant names:

• chr11-810882-G-T
• rs10902222
• NM_001004.4:c.123+525G>T

Variant summary

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

The NM_001004.4(RPLP2):​c.123+525G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.671 in 146,366 control chromosomes in the GnomAD database, including 33,069 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 0.67 (33069 hom., cov: 24)
• Consequence: RPLP2 NM_001004.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.629
• Publications: 38 publications found

Genes affected

RPLP2 (HGNC:10377): (ribosomal protein lateral stalk subunit P2) 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 phosphoprotein that is a component of the 60S subunit. The protein, which is a functional equivalent of the E. coli L7/L12 ribosomal protein, belongs to the L12P family of ribosomal proteins. It plays an important role in the elongation step of protein synthesis. Unlike most ribosomal proteins, which are basic, the encoded protein is acidic. Its C-terminal end is nearly identical to the C-terminal ends of the ribosomal phosphoproteins P0 and P1. The P2 protein can interact with P0 and P1 to form a pentameric complex consisting of P1 and P2 dimers, and a P0 monomer. The protein is located in the cytoplasm. 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.699 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001004.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RPLP2	NM_001004.4	MANE Select	c.123+525G>T		intron	N/A	NP_000995.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RPLP2	ENST00000321153.9	TSL:1 MANE Select	c.123+525G>T		intron	N/A	ENSP00000322419.4
	RPLP2	ENST00000530797.6	TSL:1	c.123+525G>T		intron	N/A	ENSP00000431240.1
	RPLP2	ENST00000718237.1		c.123+525G>T		intron	N/A	ENSP00000520682.1

Frequencies

GnomAD3 genomes AF: 0.671 AC: 98084 AN: 146284 Hom.: 33027 Cov.: 24

Gnomad AFR AF: 0.699

Gnomad AMI AF: 0.733

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.609

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.664

Gnomad MID AF: 0.564

Gnomad NFE AF: 0.674

Gnomad OTH AF: 0.633

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.671 AC: 98166 AN: 146366 Hom.: 33069 Cov.: 24 AF XY: 0.665 AC XY: 46995 AN XY: 70644

African (AFR) AF: 0.700 AC: 27737 AN: 39648

American (AMR) AF: 0.711 AC: 10427 AN: 14674

Ashkenazi Jewish (ASJ) AF: 0.473 AC: 1628 AN: 3444

East Asian (EAS) AF: 0.609 AC: 3082 AN: 5058

South Asian (SAS) AF: 0.486 AC: 2258 AN: 4646

European-Finnish (FIN) AF: 0.664 AC: 5694 AN: 8570

Middle Eastern (MID) AF: 0.559 AC: 162 AN: 290

European-Non Finnish (NFE) AF: 0.674 AC: 45211 AN: 67086

Other (OTH) AF: 0.638 AC: 1309 AN: 2052

Alfa AF: 0.664 Hom.: 79268

Bravo AF: 0.676

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.9
DANN	Benign	0.17
PhyloP100		-0.63
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: rs10902222; hg19: chr11-810882;