NM_002948.5:c.87G>T

Variant names:

• chr3-23917946-G-T
• NM_002948.5:c.87G>T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_002948.5(RPL15):​c.87G>T​(p.Gln29His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: RPL15 NM_002948.5 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 1.63

Genes affected

RPL15 (HGNC:10306): (ribosomal protein L15) Ribosomes, the organelles that catalyze protein synthesis, consist of a small 40S subunit and a large 60S subunit. Together these subunits are composed of four RNA species and approximately 80 structurally distinct proteins. This gene encodes a member of the L15E family of ribosomal proteins and a component of the 60S subunit. This gene shares sequence similarity with the yeast ribosomal protein YL10 gene. Elevated expression of this gene has been observed in esophageal tumors and gastric cancer tissues, and deletion of this gene has been observed in a Diamond-Blackfan anemia (DBA) patient. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. [provided by RefSeq, Mar 2017]

NKIRAS1 (HGNC:17899): (NFKB inhibitor interacting Ras like 1) Predicted to enable GTPase activating protein binding activity. Predicted to be involved in I-kappaB kinase/NF-kappaB signaling. Predicted to act upstream of or within several processes, including Ral protein signal transduction; lung alveolus development; and surfactant homeostasis. Located in cytosol and endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 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
RPL15	NM_002948.5	c.87G>T	p.Gln29His	missense_variant	Exon 2 of 4	ENST00000307839.10	NP_002939.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RPL15	ENST00000307839.10	c.87G>T	p.Gln29His	missense_variant	Exon 2 of 4	1	NM_002948.5	ENSP00000309334.5

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Uncertain:1

Apr 23, 2019

GeneDx

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Has not been previously published as pathogenic or benign to our knowledge; Not observed in large population cohorts (Lek et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.60
BayesDel_addAF	Pathogenic	0.30	D
BayesDel_noAF	Pathogenic	0.20
CADD	Uncertain	23
DANN	Uncertain	0.98
DEOGEN2	Benign	0.19	T;T;T;T;T;T;.;.;.;T;T;.;T
Eigen	Benign	-0.43
Eigen_PC	Benign	-0.37
FATHMM_MKL	Uncertain	0.80	D
LIST_S2	Benign	0.85	.;T;T;T;.;.;T;T;T;.;.;T;.
M_CAP	Benign	0.071	D
MetaRNN	Uncertain	0.44	T;T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM	Benign	-0.69	T
MutationAssessor	Uncertain	2.4	M;.;M;.;M;M;.;M;.;M;M;.;M
PrimateAI	Pathogenic	0.82	D
PROVEAN	Uncertain	-2.4	N;D;.;N;N;N;.;D;N;N;.;.;N
REVEL	Uncertain	0.29
Sift	Benign	0.073	T;T;.;T;T;T;.;T;T;T;.;.;T
Sift4G	Uncertain	0.036	D;D;D;D;D;D;.;D;D;D;.;.;D
Polyphen		0.0	B;.;B;.;B;B;.;.;.;B;B;.;B
Vest4		0.77
MutPred		0.56		Gain of catalytic residue at Q29 (P = 0.1715);Gain of catalytic residue at Q29 (P = 0.1715);Gain of catalytic residue at Q29 (P = 0.1715);Gain of catalytic residue at Q29 (P = 0.1715);Gain of catalytic residue at Q29 (P = 0.1715);Gain of catalytic residue at Q29 (P = 0.1715);Gain of catalytic residue at Q29 (P = 0.1715);Gain of catalytic residue at Q29 (P = 0.1715);Gain of catalytic residue at Q29 (P = 0.1715);Gain of catalytic residue at Q29 (P = 0.1715);Gain of catalytic residue at Q29 (P = 0.1715);Gain of catalytic residue at Q29 (P = 0.1715);Gain of catalytic residue at Q29 (P = 0.1715);
MVP		0.91
MPC		1.5
ClinPred		0.70	D
GERP RS		-0.51
Varity_R		0.15
gMVP		0.90

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.26		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.26		Position offset: 27

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr3-23959437;