20-16586557-C-T

Variant names:

• chr20-16586557-C-T
• rs3746786
• ENST00000457002.1:n.137G>A

Variant summary

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

The ENST00000457002.1(RPLP0P1):​n.137G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.527 in 152,266 control chromosomes in the GnomAD database, including 21,657 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 0.53 (21570 hom., cov: 32)
  • Exomes 𝑓: 0.52 (87 hom.)
• Consequence: RPLP0P1 ENST00000457002.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0310

Genes affected

RPLP0P1 (HGNC:16585): (ribosomal protein lateral stalk subunit P0 pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.621 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RPLP0P1		n.16586557C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RPLP0P1	ENST00000457002.1	n.137G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.526 AC: 79785 AN: 151560 Hom.: 21541 Cov.: 32

Gnomad AFR AF: 0.627

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.595

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.478

GnomAD4 exome AF: 0.517 AC: 304 AN: 588 Hom.: 87 Cov.: 0 AF XY: 0.494 AC XY: 178 AN XY: 360

Gnomad4 AFR exome AF: 0.417

Gnomad4 AMR exome AF: 1.00

Gnomad4 ASJ exome AF: 0.667

Gnomad4 EAS exome AF: 0.389

Gnomad4 SAS exome AF: 0.250

Gnomad4 FIN exome AF: 0.617

Gnomad4 NFE exome AF: 0.465

Gnomad4 OTH exome AF: 0.447

GnomAD4 genome AF: 0.527 AC: 79868 AN: 151678 Hom.: 21570 Cov.: 32 AF XY: 0.528 AC XY: 39139 AN XY: 74134

Gnomad4 AFR AF: 0.627

Gnomad4 AMR AF: 0.467

Gnomad4 ASJ AF: 0.408

Gnomad4 EAS AF: 0.594

Gnomad4 SAS AF: 0.485

Gnomad4 FIN AF: 0.596

Gnomad4 NFE AF: 0.475

Gnomad4 OTH AF: 0.481

Alfa AF: 0.461 Hom.: 7576

Bravo AF: 0.525

Asia WGS AF: 0.549 AC: 1906 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	4.3
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3746786; hg19: chr20-16567202;