rs1122590

Variant names:

• chr12-65781076-A-G
• rs1122590
• ENST00000489520.2:n.133-22045T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000489520.2(RPSAP52):​n.133-22045T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 152,130 control chromosomes in the GnomAD database, including 3,703 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 (3703 hom., cov: 32)
• Consequence: RPSAP52 ENST00000489520.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.402
• Publications: 8 publications found

Genes affected

RPSAP52 (HGNC:):

RPSAP52 (HGNC:35752): (ribosomal protein SA pseudogene 52)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RPSAP52	NR_026825.2	n.133-22045T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RPSAP52	ENST00000489520.2	n.133-22045T>C		intron_variant	Intron 1 of 1	1
RPSAP52	ENST00000806297.1	n.113+45767T>C		intron_variant	Intron 1 of 1
RPSAP52	ENST00000806298.1	n.135-5197T>C		intron_variant	Intron 1 of 2
RPSAP52	ENST00000806299.1	n.255-22045T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27831 AN: 152012 Hom.: 3681 Cov.: 32

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.0704

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.183 AC: 27898 AN: 152130 Hom.: 3703 Cov.: 32 AF XY: 0.182 AC XY: 13533 AN XY: 74388

African (AFR) AF: 0.380 AC: 15752 AN: 41460

American (AMR) AF: 0.113 AC: 1732 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 757 AN: 3468

East Asian (EAS) AF: 0.107 AC: 553 AN: 5174

South Asian (SAS) AF: 0.182 AC: 872 AN: 4802

European-Finnish (FIN) AF: 0.0704 AC: 746 AN: 10600

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.102 AC: 6957 AN: 68014

Other (OTH) AF: 0.187 AC: 396 AN: 2114

Alfa AF: 0.150 Hom.: 455

Bravo AF: 0.194

Asia WGS AF: 0.161 AC: 558 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.2
DANN	Benign	0.24
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs1122590; hg19: chr12-66174856;