rs7270994

Variant names:

• chr20-4675170-G-A
• rs7270994
• ENST00000652447.1:n.87+9892C>T

Your query was ambiguous. Multiple possible variants found:

• chr20-4675170-G-A
• chr20-4675170-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+9892C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 152,122 control chromosomes in the GnomAD database, including 2,973 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 0.17 (2973 hom., cov: 32)
• Consequence: RPS4XP2 ENST00000652447.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08

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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.31 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+9892C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26286 AN: 152004 Hom.: 2967 Cov.: 32

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.0341

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.173 AC: 26319 AN: 152122 Hom.: 2973 Cov.: 32 AF XY: 0.175 AC XY: 13034 AN XY: 74368

Gnomad4 AFR AF: 0.314

Gnomad4 AMR AF: 0.154

Gnomad4 ASJ AF: 0.109

Gnomad4 EAS AF: 0.0340

Gnomad4 SAS AF: 0.145

Gnomad4 FIN AF: 0.166

Gnomad4 NFE AF: 0.110

Gnomad4 OTH AF: 0.144

Alfa AF: 0.110 Hom.: 396

Bravo AF: 0.177

Asia WGS AF: 0.105 AC: 370 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	6.1
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7270994; hg19: chr20-4655816;