12-65767191-A-G

Variant names:

• chr12-65767191-A-G
• rs10784496
• ENST00000489520.2:n.133-8160T>C

Variant summary

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

The ENST00000489520.2(RPSAP52):​n.133-8160T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.565 in 152,044 control chromosomes in the GnomAD database, including 25,555 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 0.56 (25555 hom., cov: 32)
• Consequence: RPSAP52 ENST00000489520.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.43
• Publications: 10 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=-0.66).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.747 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000489520.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RPSAP52	NR_026825.2		n.133-8160T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RPSAP52	ENST00000489520.2	TSL:1	n.133-8160T>C		intron	N/A
	RPSAP52	ENST00000806297.1		n.114-37912T>C		intron	N/A
	RPSAP52	ENST00000806298.1		n.239-8160T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.564 AC: 85750 AN: 151928 Hom.: 25500 Cov.: 32

Gnomad AFR AF: 0.754

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.714

Gnomad SAS AF: 0.580

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.520

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

GnomAD4 genome AF: 0.565 AC: 85865 AN: 152044 Hom.: 25555 Cov.: 32 AF XY: 0.566 AC XY: 42026 AN XY: 74316

African (AFR) AF: 0.754 AC: 31294 AN: 41490

American (AMR) AF: 0.582 AC: 8877 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.444 AC: 1543 AN: 3472

East Asian (EAS) AF: 0.714 AC: 3675 AN: 5146

South Asian (SAS) AF: 0.578 AC: 2789 AN: 4824

European-Finnish (FIN) AF: 0.434 AC: 4593 AN: 10580

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.461 AC: 31349 AN: 67954

Other (OTH) AF: 0.526 AC: 1111 AN: 2114

Alfa AF: 0.495 Hom.: 89364

Bravo AF: 0.585

Asia WGS AF: 0.681 AC: 2369 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	17
DANN	Benign	0.62
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs10784496; hg19: chr12-66160971;