rs943133

Variant names:

• chr1-153225243-G-A
• rs943133
• ENST00000445179.1:n.164G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000445179.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RPLP0P4	ENST00000445179.1	TSL:6	n.164G>A		non_coding_transcript_exon	Exon 1 of 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

African (AFR) AF: 0.0636 AC: 321 AN: 5046

American (AMR) AF: 0.129 AC: 1823 AN: 14154

Ashkenazi Jewish (ASJ) AF: 0.141 AC: 643 AN: 4568

East Asian (EAS) AF: 0.0437 AC: 403 AN: 9230

South Asian (SAS) AF: 0.189 AC: 4137 AN: 21932

European-Finnish (FIN) AF: 0.277 AC: 6794 AN: 24534

Middle Eastern (MID) AF: 0.151 AC: 312 AN: 2072

European-Non Finnish (NFE) AF: 0.256 AC: 26824 AN: 104702

Other (OTH) AF: 0.229 AC: 2243 AN: 9810

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

African (AFR) AF: 0.0757 AC: 3145 AN: 41564

American (AMR) AF: 0.186 AC: 2841 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 568 AN: 3472

East Asian (EAS) AF: 0.0667 AC: 345 AN: 5174

South Asian (SAS) AF: 0.189 AC: 909 AN: 4822

European-Finnish (FIN) AF: 0.278 AC: 2944 AN: 10596

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.295 AC: 20072 AN: 67992

Other (OTH) AF: 0.215 AC: 452 AN: 2104

Alfa AF: 0.254 Hom.: 1286

Bravo AF: 0.194

Asia WGS AF: 0.120 AC: 422 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	2.5
DANN	Benign	0.50
PhyloP100		6.9

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs943133;

hg19: chr1-153197719;