ENST00000489520.2:n.132+4550T>C

Variant names:

• chr12-65822293-A-G
• rs7977687
• ENST00000489520.2:n.132+4550T>C

Variant summary

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

The ENST00000489520.2(RPSAP52):​n.132+4550T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 152,234 control chromosomes in the GnomAD database, including 2,635 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 (2635 hom., cov: 32)
• Consequence: RPSAP52 ENST00000489520.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.221
• Publications: 5 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RPSAP52	NR_026825.2	n.132+4550T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RPSAP52	ENST00000489520.2	n.132+4550T>C		intron_variant	Intron 1 of 1	1
RPSAP52	ENST00000806297.1	n.113+4550T>C		intron_variant	Intron 1 of 1
RPSAP52	ENST00000806298.1	n.134+4550T>C		intron_variant	Intron 1 of 2
RPSAP52	ENST00000806299.1	n.254+2895T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20505 AN: 152116 Hom.: 2622 Cov.: 32

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.0430

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.0440

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0363

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.135 AC: 20540 AN: 152234 Hom.: 2635 Cov.: 32 AF XY: 0.137 AC XY: 10180 AN XY: 74440

African (AFR) AF: 0.319 AC: 13227 AN: 41500

American (AMR) AF: 0.104 AC: 1586 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0430 AC: 149 AN: 3468

East Asian (EAS) AF: 0.227 AC: 1176 AN: 5184

South Asian (SAS) AF: 0.241 AC: 1163 AN: 4820

European-Finnish (FIN) AF: 0.0440 AC: 466 AN: 10602

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0363 AC: 2470 AN: 68034

Other (OTH) AF: 0.129 AC: 272 AN: 2116

Alfa AF: 0.0920 Hom.: 245

Bravo AF: 0.145

Asia WGS AF: 0.271 AC: 937 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.1
DANN	Benign	0.73
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs7977687; hg19: chr12-66216073;