rs2859720

Variant names:

• chr20-4673939-G-A
• rs2859720
• ENST00000652447.1:n.87+11123C>T

Your query was ambiguous. Multiple possible variants found:

• chr20-4673939-G-A
• chr20-4673939-G-T

Variant summary

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

The ENST00000652447.1(RPS4XP2):​n.87+11123C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.671 in 151,956 control chromosomes in the GnomAD database, including 35,280 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 (35280 hom., cov: 31)
• Consequence: RPS4XP2 ENST00000652447.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0480

Genes affected

RPS4XP2 (HGNC:16563): (ribosomal protein S4X pseudogene 2)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.843 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RPS4XP2	ENST00000652447.1	n.87+11123C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.671 AC: 101902 AN: 151836 Hom.: 35212 Cov.: 31

Gnomad AFR AF: 0.850

Gnomad AMI AF: 0.627

Gnomad AMR AF: 0.674

Gnomad ASJ AF: 0.504

Gnomad EAS AF: 0.569

Gnomad SAS AF: 0.549

Gnomad FIN AF: 0.636

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.595

Gnomad OTH AF: 0.630

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.671 AC: 102033 AN: 151956 Hom.: 35280 Cov.: 31 AF XY: 0.669 AC XY: 49692 AN XY: 74266

Gnomad4 AFR AF: 0.850

Gnomad4 AMR AF: 0.674

Gnomad4 ASJ AF: 0.504

Gnomad4 EAS AF: 0.569

Gnomad4 SAS AF: 0.548

Gnomad4 FIN AF: 0.636

Gnomad4 NFE AF: 0.595

Gnomad4 OTH AF: 0.632

Alfa AF: 0.606 Hom.: 19242

Bravo AF: 0.685

Asia WGS AF: 0.582 AC: 2024 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.7
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2859720; hg19: chr20-4654585;