rs943133

chr1-153225243-G-A

Variant summary

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

The ENST00000445179.1(RPLP0P4):n.164G>A variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.215 in 348,280 control chromosomes in the GnomAD database, including 9,697 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 0.21 (4003 hom., cov: 33)
  • Exomes 𝑓: 0.22 (5694 hom.)
• Consequence: RPLP0P4 ENST00000445179.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.92

Genes affected

RPLP0P4 (HGNC:36489): (ribosomal protein lateral stalk subunit P0 pseudogene 4)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.292 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
RPLP0P4	ENST00000445179.1	n.164G>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31495 AN: 152114 Hom.: 4000 Cov.: 33

Gnomad AFR AF: 0.0757

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.0667

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.218

GnomAD4 exome AF: 0.222 AC: 43500 AN: 196048 Hom.: 5694 Cov.: 0 AF XY: 0.223 AC XY: 23609 AN XY: 105870

Gnomad4 AFR exome AF: 0.0636

Gnomad4 AMR exome AF: 0.129

Gnomad4 ASJ exome AF: 0.141

Gnomad4 EAS exome AF: 0.0437

Gnomad4 SAS exome AF: 0.189

Gnomad4 FIN exome AF: 0.277

Gnomad4 NFE exome AF: 0.256

Gnomad4 OTH exome AF: 0.229

GnomAD4 genome AF: 0.207 AC: 31507 AN: 152232 Hom.: 4003 Cov.: 33 AF XY: 0.204 AC XY: 15214 AN XY: 74440

Gnomad4 AFR AF: 0.0757

Gnomad4 AMR AF: 0.186

Gnomad4 ASJ AF: 0.164

Gnomad4 EAS AF: 0.0667

Gnomad4 SAS AF: 0.189

Gnomad4 FIN AF: 0.278

Gnomad4 NFE AF: 0.295

Gnomad4 OTH AF: 0.215

Alfa AF: 0.258 Hom.: 1285

Bravo AF: 0.194

Asia WGS AF: 0.120 AC: 422 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
Cadd	Benign	2.5
Dann	Benign	0.50

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs943133; hg19: chr1-153197719;