rs17084051

Variant names:

• chr4-54221414-C-A
• rs17084051
• ENST00000507166.5:c.1018-53511C>A

Your query was ambiguous. Multiple possible variants found:

• chr4-54221414-C-A
• chr4-54221414-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000507166.5(ENSG00000282278):​c.1018-53511C>A variant causes a intron 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: ENSG00000282278 ENST00000507166.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.57
• Publications: 26 publications found

Genes affected

ENSG00000282278 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
RPL22P13		n.54221414C>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000282278	ENST00000507166.5	c.1018-53511C>A		intron_variant	Intron 12 of 23	2		ENSP00000423325.1
RPL22P13	ENST00000493291.1	n.289C>A		non_coding_transcript_exon_variant	Exon 1 of 1	6

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

African (AFR) AF: 0.299 AC: 2991 AN: 9990

American (AMR) AF: 0.347 AC: 5313 AN: 15322

Ashkenazi Jewish (ASJ) AF: 0.0971 AC: 1215 AN: 12510

East Asian (EAS) AF: 0.167 AC: 3749 AN: 22398

South Asian (SAS) AF: 0.222 AC: 9312 AN: 41940

European-Finnish (FIN) AF: 0.200 AC: 7457 AN: 37290

Middle Eastern (MID) AF: 0.175 AC: 565 AN: 3226

European-Non Finnish (NFE) AF: 0.193 AC: 42184 AN: 219048

Other (OTH) AF: 0.203 AC: 4212 AN: 20748

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

African (AFR) AF: 0.326 AC: 13493 AN: 41390

American (AMR) AF: 0.331 AC: 5046 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 351 AN: 3468

East Asian (EAS) AF: 0.198 AC: 1025 AN: 5170

South Asian (SAS) AF: 0.255 AC: 1228 AN: 4820

European-Finnish (FIN) AF: 0.207 AC: 2181 AN: 10554

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.209 AC: 14236 AN: 67990

Other (OTH) AF: 0.218 AC: 460 AN: 2108

Alfa AF: 0.219 Hom.: 17721

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
PhyloP100		1.6
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: rs17084051; hg19: chr4-55087581; COSMIC: COSV72387830;