rs6052761

Variant names:

• chr20-4676371-T-C
• rs6052761
• ENST00000652447.1:n.87+8691A>G

Your query was ambiguous. Multiple possible variants found:

• chr20-4676371-T-C
• chr20-4676371-T-G

Variant summary

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

The ENST00000652447.1(RPS4XP2):​n.87+8691A>G 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 152,206 control chromosomes in the GnomAD database, including 3,086 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 (3086 hom., cov: 32)
• Consequence: RPS4XP2 ENST00000652447.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.317 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+8691A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26684 AN: 152088 Hom.: 3078 Cov.: 32

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.0358

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.176 AC: 26717 AN: 152206 Hom.: 3086 Cov.: 32 AF XY: 0.178 AC XY: 13212 AN XY: 74414

Gnomad4 AFR AF: 0.321

Gnomad4 AMR AF: 0.154

Gnomad4 ASJ AF: 0.111

Gnomad4 EAS AF: 0.0357

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.166

Gnomad4 NFE AF: 0.111

Gnomad4 OTH AF: 0.145

Alfa AF: 0.112 Hom.: 1522

Bravo AF: 0.181

Asia WGS AF: 0.107 AC: 378 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.75
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6052761; hg19: chr20-4657017;