NM_005617.4:c.311+495G>A

Variant names:

• chr5-150446307-C-T
• rs13177918
• NM_005617.4:c.311+495G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005617.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RPS14	NM_005617.4	MANE Select	c.311+495G>A		intron	N/A	NP_005608.1	P62263
	RPS14	NM_001025070.2		c.311+495G>A		intron	N/A	NP_001020241.1	P62263
	RPS14	NM_001025071.2		c.311+495G>A		intron	N/A	NP_001020242.1	P62263

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RPS14	ENST00000407193.7	TSL:2 MANE Select	c.311+495G>A		intron	N/A	ENSP00000385425.1	P62263
	RPS14	ENST00000312037.6	TSL:1	c.311+495G>A		intron	N/A	ENSP00000311028.5	P62263
	RPS14	ENST00000401695.8	TSL:1	c.311+495G>A		intron	N/A	ENSP00000385958.3	P62263

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

African (AFR) AF: 0.0819 AC: 3397 AN: 41490

American (AMR) AF: 0.185 AC: 2819 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 466 AN: 3470

East Asian (EAS) AF: 0.229 AC: 1186 AN: 5174

South Asian (SAS) AF: 0.337 AC: 1625 AN: 4822

European-Finnish (FIN) AF: 0.245 AC: 2586 AN: 10556

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.221 AC: 15024 AN: 67932

Other (OTH) AF: 0.181 AC: 382 AN: 2110

Alfa AF: 0.208 Hom.: 9472

Bravo AF: 0.169

Asia WGS AF: 0.282 AC: 978 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.7
DANN	Benign	0.51
PhyloP100		-1.3
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: rs13177918; hg19: chr5-149825870;