rs6139516

Variant names:

• chr20-4668630-A-G
• rs6139516
• ENST00000652447.1:n.87+16432T>C

Variant summary

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

The ENST00000652447.1(RPS4XP2):​n.87+16432T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.274 in 152,118 control chromosomes in the GnomAD database, including 6,523 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 0.27 (6523 hom., cov: 32)
• Consequence: RPS4XP2 ENST00000652447.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.534

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.432 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+16432T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.274 AC: 41581 AN: 152000 Hom.: 6509 Cov.: 32

Gnomad AFR AF: 0.438

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.274 AC: 41637 AN: 152118 Hom.: 6523 Cov.: 32 AF XY: 0.275 AC XY: 20453 AN XY: 74384

Gnomad4 AFR AF: 0.438

Gnomad4 AMR AF: 0.200

Gnomad4 ASJ AF: 0.227

Gnomad4 EAS AF: 0.270

Gnomad4 SAS AF: 0.203

Gnomad4 FIN AF: 0.251

Gnomad4 NFE AF: 0.204

Gnomad4 OTH AF: 0.261

Alfa AF: 0.210 Hom.: 4549

Bravo AF: 0.278

Asia WGS AF: 0.269 AC: 935 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.41
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: rs6139516; hg19: chr20-4649276;