chr4-54221414-C-A

Variant names:

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

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000507166.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000282278	ENST00000507166.5	TSL:2	c.1018-53511C>A		intron	N/A	ENSP00000423325.1
	RPL22P13	ENST00000493291.1	TSL:6	n.289C>A		non_coding_transcript_exon	Exon 1 of 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

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 v4.9

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;