rs754547606

Variant names:

• chr3-51994040-C-A
• NM_000992.3:c.189G>T

Your query was ambiguous. Multiple possible variants found:

• chr3-51994040-C-A
• chr3-51994040-C-G

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_000992.3(RPL29):​c.189G>T​(p.Lys63Asn) variant causes a missense change. The variant allele was found at a frequency of 0.000000691 in 1,448,058 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 6.9e-7 (0 hom.)
• Consequence: RPL29 NM_000992.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.82

Genes affected

RPL29 (HGNC:10331): (ribosomal protein L29) 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 cytoplasmic ribosomal protein that is a component of the 60S subunit. The protein belongs to the L29E family of ribosomal proteins. The protein is also a peripheral membrane protein expressed on the cell surface that directly binds heparin. Although this gene was previously reported to map to 3q29-qter, it is believed that it is located at 3p21.3-p21.2. 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

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.31770796).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RPL29	NM_000992.3	c.189G>T	p.Lys63Asn	missense_variant	Exon 4 of 4	ENST00000294189.11	NP_000983.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RPL29	ENST00000294189.11	c.189G>T	p.Lys63Asn	missense_variant	Exon 4 of 4	1	NM_000992.3	ENSP00000294189.4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 6.91e-7 AC: 1 AN: 1448058 Hom.: 0 Cov.: 32 AF XY: 0.00000139 AC XY: 1 AN XY: 720592

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000116

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.68
BayesDel_addAF	Benign	-0.044	T
BayesDel_noAF	Benign	-0.30
CADD	Uncertain	24
DANN	Uncertain	0.99
DEOGEN2	Uncertain	0.79	.;D;D;D;D;D;D
Eigen	Benign	-0.050
Eigen_PC	Benign	-0.060
FATHMM_MKL	Uncertain	0.85	D
LIST_S2	Benign	0.65	T;.;.;.;.;.;T
M_CAP	Benign	0.023	T
MetaRNN	Benign	0.32	T;T;T;T;T;T;T
MetaSVM	Benign	-0.73	T
MutationAssessor	Pathogenic	3.1	.;M;M;M;M;M;M
PrimateAI	Uncertain	0.66	T
PROVEAN	Pathogenic	-4.5	.;D;D;D;D;D;D
REVEL	Benign	0.18
Sift	Uncertain	0.013	.;D;D;D;D;D;D
Sift4G	Uncertain	0.0080	.;D;D;D;D;D;.
Polyphen		0.22	.;B;B;B;B;B;B
Vest4		0.82, 0.78, 0.82, 0.82
MutPred		0.34		.;Gain of glycosylation at S66 (P = 0.0194);Gain of glycosylation at S66 (P = 0.0194);Gain of glycosylation at S66 (P = 0.0194);Gain of glycosylation at S66 (P = 0.0194);Gain of glycosylation at S66 (P = 0.0194);Gain of glycosylation at S66 (P = 0.0194);
MVP		0.68
MPC		1.5
ClinPred		0.94	D
GERP RS		2.9
Varity_R		0.26
gMVP		0.35

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr3-52028056;