rs17084051

chr4-54221414-C-A

Variant summary

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

The ENST00000493291.1(RPL22P13):n.289C>A 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 0.216 in 534,414 control chromosomes in the GnomAD database, including 13,463 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 0.25 (5148 hom., cov: 32)
  • Exomes 𝑓: 0.20 (8315 hom.)
• Consequence: RPL22P13 ENST00000493291.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.57

Genes affected

RPL22P13 (HGNC:36352): (ribosomal protein L22 pseudogene 13)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RPL22P13	ENST00000493291.1	n.289C>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.251 AC: 38146 AN: 151824 Hom.: 5141 Cov.: 32

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.221

GnomAD4 exome AF: 0.201 AC: 76998 AN: 382472 Hom.: 8315 Cov.: 0 AF XY: 0.199 AC XY: 41062 AN XY: 206162

Gnomad4 AFR exome AF: 0.299

Gnomad4 AMR exome AF: 0.347

Gnomad4 ASJ exome AF: 0.0971

Gnomad4 EAS exome AF: 0.167

Gnomad4 SAS exome AF: 0.222

Gnomad4 FIN exome AF: 0.200

Gnomad4 NFE exome AF: 0.193

Gnomad4 OTH exome AF: 0.203

GnomAD4 genome AF: 0.251 AC: 38197 AN: 151942 Hom.: 5148 Cov.: 32 AF XY: 0.251 AC XY: 18668 AN XY: 74250

Gnomad4 AFR AF: 0.326

Gnomad4 AMR AF: 0.331

Gnomad4 ASJ AF: 0.101

Gnomad4 EAS AF: 0.198

Gnomad4 SAS AF: 0.255

Gnomad4 FIN AF: 0.207

Gnomad4 NFE AF: 0.209

Gnomad4 OTH AF: 0.218

Alfa AF: 0.211 Hom.: 7820

Bravo AF: 0.264

Asia WGS AF: 0.253 AC: 882 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
Cadd	Benign	2.3
Dann	Benign	0.55

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: rs17084051; hg19: chr4-55087581; COSMIC: COSV72387830;