chr5-150446307-C-T

Position:

• chr5-150446307-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005617.4(RPS14):​c.311+495G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 152,038 control chromosomes in the GnomAD database, including 2,956 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 0.18 (2956 hom., cov: 32)
• Consequence: RPS14 NM_005617.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34

Genes affected

RPS14 (HGNC:10387): (ribosomal protein S14) 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 S11P family of ribosomal proteins. It is located in the cytoplasm. Transcript variants utilizing alternative transcription initiation sites have been described in the literature. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. In Chinese hamster ovary cells, mutations in this gene can lead to resistance to emetine, a protein synthesis inhibitor. Multiple alternatively spliced transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RPS14	NM_005617.4	c.311+495G>A		intron_variant		ENST00000407193.7	NP_005608.1
RPS14	NM_001025070.2	c.311+495G>A		intron_variant			NP_001020241.1
RPS14	NM_001025071.2	c.311+495G>A		intron_variant			NP_001020242.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RPS14	ENST00000407193.7	c.311+495G>A		intron_variant		2	NM_005617.4	ENSP00000385425	P1

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27633 AN: 151920 Hom.: 2949 Cov.: 32

Gnomad AFR AF: 0.0822

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.182 AC: 27646 AN: 152038 Hom.: 2956 Cov.: 32 AF XY: 0.187 AC XY: 13888 AN XY: 74310

Gnomad4 AFR AF: 0.0819

Gnomad4 AMR AF: 0.185

Gnomad4 ASJ AF: 0.134

Gnomad4 EAS AF: 0.229

Gnomad4 SAS AF: 0.337

Gnomad4 FIN AF: 0.245

Gnomad4 NFE AF: 0.221

Gnomad4 OTH AF: 0.181

Alfa AF: 0.214 Hom.: 3263

Bravo AF: 0.169

Asia WGS AF: 0.282 AC: 978 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.7
DANN	Benign	0.51

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: rs13177918; hg19: chr5-149825870;