ENST00000524864.1:n.192A>G

Variant names:

• chr11-119018475-T-C
• rs11217125
• ENST00000937795.1:c.-191A>G

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The ENST00000524864.1(RPS25):​n.192A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.261 in 751,086 control chromosomes in the GnomAD database, including 27,014 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.28 (6446 hom., cov: 35)
  • Exomes 𝑓: 0.26 (20568 hom.)
• Consequence: RPS25 ENST00000524864.1 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -1.89
• Publications: 18 publications found

Genes affected

RPS25 (HGNC:10413): (ribosomal protein S25) 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 S25E family of ribosomal proteins. It 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]

ENSG00000300421 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BP6: Variant 11-119018475-T-C is Benign according to our data. Variant chr11-119018475-T-C is described in ClinVar as Benign. ClinVar VariationId is 1226681.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.374 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000524864.1. 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
	RPS25	NM_001028.3	MANE Select	c.-191A>G		upstream_gene	N/A	NP_001019.1	P62851

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RPS25	ENST00000937795.1		c.-191A>G		5_prime_UTR	Exon 1 of 5	ENSP00000607854.1
	RPS25	ENST00000942362.1		c.-191A>G		5_prime_UTR	Exon 1 of 5	ENSP00000612421.1
	RPS25	ENST00000937796.1		c.-191A>G		5_prime_UTR	Exon 1 of 5	ENSP00000607855.1

Frequencies

GnomAD3 genomes AF: 0.281 AC: 42785 AN: 152008 Hom.: 6423 Cov.: 35

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.0737

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.275

GnomAD4 exome AF: 0.256 AC: 153154 AN: 598960 Hom.: 20568 Cov.: 8 AF XY: 0.259 AC XY: 81282 AN XY: 314256

African (AFR) AF: 0.375 AC: 5659 AN: 15086

American (AMR) AF: 0.200 AC: 4649 AN: 23286

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 3346 AN: 15906

East Asian (EAS) AF: 0.101 AC: 3244 AN: 32186

South Asian (SAS) AF: 0.317 AC: 16837 AN: 53178

European-Finnish (FIN) AF: 0.261 AC: 8481 AN: 32490

Middle Eastern (MID) AF: 0.234 AC: 704 AN: 3006

European-Non Finnish (NFE) AF: 0.260 AC: 101958 AN: 392552

Other (OTH) AF: 0.265 AC: 8276 AN: 31270

GnomAD4 genome AF: 0.282 AC: 42849 AN: 152126 Hom.: 6446 Cov.: 35 AF XY: 0.280 AC XY: 20809 AN XY: 74344

African (AFR) AF: 0.379 AC: 15706 AN: 41494

American (AMR) AF: 0.236 AC: 3603 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.196 AC: 681 AN: 3470

East Asian (EAS) AF: 0.0738 AC: 382 AN: 5174

South Asian (SAS) AF: 0.329 AC: 1586 AN: 4824

European-Finnish (FIN) AF: 0.273 AC: 2892 AN: 10576

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.252 AC: 17145 AN: 67984

Other (OTH) AF: 0.278 AC: 587 AN: 2114

Alfa AF: 0.261 Hom.: 13249

Bravo AF: 0.279

Asia WGS AF: 0.239 AC: 835 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.24
DANN	Benign	0.39
PhyloP100		-1.9
PromoterAI		-0.058	Neutral
Mutation Taster		=300/0	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: rs11217125; hg19: chr11-118889185;