rs10485513

Variant names:

• chr20-4674956-A-G
• rs10485513
• ENST00000652447.1:n.87+10106T>C

Variant summary

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

The ENST00000652447.1(RPS4XP2):​n.87+10106T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 152,226 control chromosomes in the GnomAD database, including 3,037 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 0.18 (3037 hom., cov: 33)
• Consequence: RPS4XP2 ENST00000652447.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.711

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.312 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+10106T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26782 AN: 152108 Hom.: 3033 Cov.: 33

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.0160

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.176 AC: 26813 AN: 152226 Hom.: 3037 Cov.: 33 AF XY: 0.178 AC XY: 13257 AN XY: 74420

Gnomad4 AFR AF: 0.317

Gnomad4 AMR AF: 0.162

Gnomad4 ASJ AF: 0.116

Gnomad4 EAS AF: 0.0158

Gnomad4 SAS AF: 0.145

Gnomad4 FIN AF: 0.166

Gnomad4 NFE AF: 0.114

Gnomad4 OTH AF: 0.148

Alfa AF: 0.131 Hom.: 445

Bravo AF: 0.182

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.4
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10485513; hg19: chr20-4655602;