rs2009092

Positions:

• chr20-18504768-C-G
• chr20-18504768-C-T

Variant summary

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

The ENST00000415286.1(RPS19P1):​n.136C>G 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 0.763 in 1,604,986 control chromosomes in the GnomAD database, including 475,776 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 0.67 (35625 hom., cov: 34)
  • Exomes 𝑓: 0.77 (440151 hom.)
• Consequence: RPS19P1 ENST00000415286.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.63

Genes affected

RPS19P1 (HGNC:16534): (ribosomal protein S19 pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.791 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
RPS19P1	ENST00000415286.1	n.136C>G		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.666 AC: 101336 AN: 152076 Hom.: 35625 Cov.: 34

Gnomad AFR AF: 0.446

Gnomad AMI AF: 0.816

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.707

Gnomad EAS AF: 0.545

Gnomad SAS AF: 0.757

Gnomad FIN AF: 0.770

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.796

Gnomad OTH AF: 0.671

GnomAD4 exome AF: 0.773 AC: 1122907 AN: 1452792 Hom.: 440151 Cov.: 34 AF XY: 0.775 AC XY: 560468 AN XY: 723254

Gnomad4 AFR exome AF: 0.440

Gnomad4 AMR exome AF: 0.530

Gnomad4 ASJ exome AF: 0.726

Gnomad4 EAS exome AF: 0.490

Gnomad4 SAS exome AF: 0.761

Gnomad4 FIN exome AF: 0.775

Gnomad4 NFE exome AF: 0.806

Gnomad4 OTH exome AF: 0.751

GnomAD4 genome AF: 0.666 AC: 101350 AN: 152194 Hom.: 35625 Cov.: 34 AF XY: 0.664 AC XY: 49400 AN XY: 74410

Gnomad4 AFR AF: 0.446

Gnomad4 AMR AF: 0.605

Gnomad4 ASJ AF: 0.707

Gnomad4 EAS AF: 0.544

Gnomad4 SAS AF: 0.759

Gnomad4 FIN AF: 0.770

Gnomad4 NFE AF: 0.796

Gnomad4 OTH AF: 0.668

Alfa AF: 0.726 Hom.: 5160

Bravo AF: 0.636

Asia WGS AF: 0.601 AC: 2090 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	7.1
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2009092; hg19: chr20-18485412;