rs1981105

Variant names:

• chr20-4633840-G-A
• rs1981105
• ENST00000652447.1:n.88-3619C>T

Variant summary

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

The ENST00000652447.1(RPS4XP2):​n.88-3619C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 152,096 control chromosomes in the GnomAD database, including 3,817 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 0.22 (3817 hom., cov: 32)
• Consequence: RPS4XP2 ENST00000652447.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.727

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 (EAS) allele frequency at 95% confidence interval = 0.378 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.88-3619C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32881 AN: 151978 Hom.: 3816 Cov.: 32

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.216 AC: 32900 AN: 152096 Hom.: 3817 Cov.: 32 AF XY: 0.222 AC XY: 16488 AN XY: 74348

Gnomad4 AFR AF: 0.158

Gnomad4 AMR AF: 0.283

Gnomad4 ASJ AF: 0.184

Gnomad4 EAS AF: 0.392

Gnomad4 SAS AF: 0.253

Gnomad4 FIN AF: 0.274

Gnomad4 NFE AF: 0.216

Gnomad4 OTH AF: 0.197

Alfa AF: 0.214 Hom.: 2003

Bravo AF: 0.214

Asia WGS AF: 0.348 AC: 1211 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.7
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1981105; hg19: chr20-4614486;