rs2009092

Variant names:

• chr20-18504768-C-G
• rs2009092
• ENST00000415286.1:n.136C>G

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
RPS19P1		n.18504768C>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RPS19P1	ENST00000415286.1	n.136C>G		non_coding_transcript_exon_variant	Exon 1 of 1	6

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

African (AFR) AF: 0.440 AC: 14547 AN: 33066

American (AMR) AF: 0.530 AC: 23660 AN: 44664

Ashkenazi Jewish (ASJ) AF: 0.726 AC: 18945 AN: 26080

East Asian (EAS) AF: 0.490 AC: 19432 AN: 39636

South Asian (SAS) AF: 0.761 AC: 65511 AN: 86050

European-Finnish (FIN) AF: 0.775 AC: 41271 AN: 53264

Middle Eastern (MID) AF: 0.736 AC: 3358 AN: 4562

European-Non Finnish (NFE) AF: 0.806 AC: 891131 AN: 1105470

Other (OTH) AF: 0.751 AC: 45052 AN: 60000

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

African (AFR) AF: 0.446 AC: 18490 AN: 41496

American (AMR) AF: 0.605 AC: 9257 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.707 AC: 2452 AN: 3468

East Asian (EAS) AF: 0.544 AC: 2816 AN: 5178

South Asian (SAS) AF: 0.759 AC: 3660 AN: 4824

European-Finnish (FIN) AF: 0.770 AC: 8164 AN: 10602

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.796 AC: 54156 AN: 68010

Other (OTH) AF: 0.668 AC: 1412 AN: 2114

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
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs2009092; hg19: chr20-18485412;