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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RPLP0P4		n.153225243G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RPLP0P4	ENST00000445179.1	n.164G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6

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 v4.3

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

Other links and lift over

dbSNP: rs943133; hg19: chr1-153197719;