14-94727040-T-G

Variant summary

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

The ENST00000488229.1(RPSAP4):n.753T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0869 in 1,409,056 control chromosomes in the GnomAD database, including 5,975 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 0.090 (649 hom., cov: 32)
  • Exomes 𝑓: 0.087 (5326 hom.)
• Consequence: RPSAP4 ENST00000488229.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.187

Genes affected

RPSAP4 (HGNC:20018): (ribosomal protein SA pseudogene 4)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.164 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RPSAP4	ENST00000488229.1	n.753T>G		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.0904 AC: 13720 AN: 151850 Hom.: 650 Cov.: 32

Gnomad AFR AF: 0.0664

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.0708

Gnomad ASJ AF: 0.0974

Gnomad EAS AF: 0.0552

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.0850

Gnomad MID AF: 0.0987

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.0913

GnomAD4 exome AF: 0.0865 AC: 108786 AN: 1257092 Hom.: 5326 Cov.: 23 AF XY: 0.0907 AC XY: 57592 AN XY: 634920

Gnomad4 AFR exome AF: 0.0616

Gnomad4 AMR exome AF: 0.0540

Gnomad4 ASJ exome AF: 0.0880

Gnomad4 EAS exome AF: 0.0643

Gnomad4 SAS exome AF: 0.156

Gnomad4 FIN exome AF: 0.0835

Gnomad4 NFE exome AF: 0.0837

Gnomad4 OTH exome AF: 0.0891

GnomAD4 genome AF: 0.0902 AC: 13711 AN: 151964 Hom.: 649 Cov.: 32 AF XY: 0.0916 AC XY: 6806 AN XY: 74294

Gnomad4 AFR AF: 0.0662

Gnomad4 AMR AF: 0.0706

Gnomad4 ASJ AF: 0.0974

Gnomad4 EAS AF: 0.0550

Gnomad4 SAS AF: 0.173

Gnomad4 FIN AF: 0.0850

Gnomad4 NFE AF: 0.106

Gnomad4 OTH AF: 0.0908

Alfa AF: 0.0400 Hom.: 47

Bravo AF: 0.0852

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
Cadd	Benign	4.2
Dann	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3814818; hg19: chr14-95193377;