rs7134682

Variant names:

• chr12-65774371-G-T
• rs7134682
• ENST00000489520.2:n.133-15340C>A

Variant summary

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

The ENST00000489520.2(RPSAP52):​n.133-15340C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.355 in 152,152 control chromosomes in the GnomAD database, including 16,905 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 0.36 (16905 hom., cov: 33)
• Consequence: RPSAP52 ENST00000489520.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0240
• Publications: 9 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=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.825 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RPSAP52	NR_026825.2	n.133-15340C>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RPSAP52	ENST00000489520.2	n.133-15340C>A		intron_variant	Intron 1 of 1	1
RPSAP52	ENST00000806297.1	n.114-45092C>A		intron_variant	Intron 1 of 1
RPSAP52	ENST00000806298.1	n.238+1405C>A		intron_variant	Intron 2 of 2
RPSAP52	ENST00000806299.1	n.255-15340C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.355 AC: 53897 AN: 152034 Hom.: 16843 Cov.: 33

Gnomad AFR AF: 0.832

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.473

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.355 AC: 54015 AN: 152152 Hom.: 16905 Cov.: 33 AF XY: 0.356 AC XY: 26466 AN XY: 74364

African (AFR) AF: 0.832 AC: 34547 AN: 41514

American (AMR) AF: 0.226 AC: 3459 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.260 AC: 900 AN: 3468

East Asian (EAS) AF: 0.473 AC: 2448 AN: 5176

South Asian (SAS) AF: 0.456 AC: 2195 AN: 4816

European-Finnish (FIN) AF: 0.107 AC: 1131 AN: 10582

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.125 AC: 8474 AN: 68000

Other (OTH) AF: 0.348 AC: 735 AN: 2114

Alfa AF: 0.191 Hom.: 11593

Bravo AF: 0.380

Asia WGS AF: 0.511 AC: 1773 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	4.3
DANN	Benign	0.64
PhyloP100		0.024

Splicing

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

Other links and lift over

dbSNP: rs7134682; hg19: chr12-66168151;