ENST00000488229.1:n.753T>G

Variant names:

• chr14-94727040-T-G
• rs3814818
• ENST00000488229.1:n.753T>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000488229.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RPSAP4	ENST00000488229.1	TSL:6	n.753T>G		non_coding_transcript_exon	Exon 1 of 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

African (AFR) AF: 0.0616 AC: 1843 AN: 29926

American (AMR) AF: 0.0540 AC: 2404 AN: 44510

Ashkenazi Jewish (ASJ) AF: 0.0880 AC: 2200 AN: 25000

East Asian (EAS) AF: 0.0643 AC: 2495 AN: 38778

South Asian (SAS) AF: 0.156 AC: 12730 AN: 81836

European-Finnish (FIN) AF: 0.0835 AC: 3252 AN: 38966

Middle Eastern (MID) AF: 0.100 AC: 405 AN: 4030

European-Non Finnish (NFE) AF: 0.0837 AC: 78667 AN: 940298

Other (OTH) AF: 0.0891 AC: 4790 AN: 53748

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

African (AFR) AF: 0.0662 AC: 2746 AN: 41460

American (AMR) AF: 0.0706 AC: 1077 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0974 AC: 338 AN: 3470

East Asian (EAS) AF: 0.0550 AC: 284 AN: 5164

South Asian (SAS) AF: 0.173 AC: 832 AN: 4800

European-Finnish (FIN) AF: 0.0850 AC: 896 AN: 10540

Middle Eastern (MID) AF: 0.0993 AC: 29 AN: 292

European-Non Finnish (NFE) AF: 0.106 AC: 7180 AN: 67952

Other (OTH) AF: 0.0908 AC: 192 AN: 2114

Alfa AF: 0.0405 Hom.: 47

Bravo AF: 0.0852

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	4.2
DANN	Benign	0.85
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs3814818; hg19: chr14-95193377;