rs2261181

Variant names:

• chr12-65818538-C-T
• rs2261181
• ENST00000489520.2:n.132+8305G>A

Variant summary

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

The ENST00000489520.2(RPSAP52):​n.132+8305G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 151,742 control chromosomes in the GnomAD database, including 1,631 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 0.13 (1631 hom., cov: 32)
• Consequence: RPSAP52 ENST00000489520.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0950
• Publications: 68 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.212 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RPSAP52	NR_026825.2	n.132+8305G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RPSAP52	ENST00000489520.2	n.132+8305G>A		intron_variant	Intron 1 of 1	1
RPSAP52	ENST00000806297.1	n.113+8305G>A		intron_variant	Intron 1 of 1
RPSAP52	ENST00000806298.1	n.134+8305G>A		intron_variant	Intron 1 of 2
RPSAP52	ENST00000806299.1	n.254+6650G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20302 AN: 151624 Hom.: 1625 Cov.: 32

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.0839

Gnomad AMR AF: 0.0951

Gnomad ASJ AF: 0.228

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.0682

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.0972

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.134 AC: 20333 AN: 151742 Hom.: 1631 Cov.: 32 AF XY: 0.135 AC XY: 9996 AN XY: 74120

African (AFR) AF: 0.216 AC: 8921 AN: 41360

American (AMR) AF: 0.0948 AC: 1445 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.228 AC: 789 AN: 3468

East Asian (EAS) AF: 0.105 AC: 542 AN: 5146

South Asian (SAS) AF: 0.181 AC: 870 AN: 4796

European-Finnish (FIN) AF: 0.0682 AC: 715 AN: 10482

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.0972 AC: 6605 AN: 67948

Other (OTH) AF: 0.153 AC: 321 AN: 2104

Alfa AF: 0.112 Hom.: 3361

Bravo AF: 0.140

Asia WGS AF: 0.143 AC: 498 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.8
DANN	Benign	0.60
PhyloP100		-0.095

Splicing

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

Other links and lift over

dbSNP: rs2261181; hg19: chr12-66212318;